I used [t] option but there is still a big space on the slide.

\documentclass[compress,serif,xcolor=dvipsnames,xetex,t]{beamer}

\definecolor{Setcolor}{HTML}{6698FF}
\usecolortheme[named=Setcolor]{structure}

\usepackage{xltxtra}
\XeTeXlinebreaklocale "th"
\defaultfontfeatures{Scale=1.4}
\renewcommand{\baselinestretch}{1.35}
\setmainfont[Script=Thai]{DilleniaUPC}

\usepackage[all,knot,color]{xy}
\xyoption{arc}
\usepackage{url}

{
\leavevmode%
\hbox{%

\end{beamercolorbox}%

\end{beamercolorbox}}%

\vskip0pt%
}

\setbeamertemplate{footline}
{
\leavevmode%
\hbox{%

\end{beamercolorbox}%
%
\end{beamercolorbox}%
%
\end{beamercolorbox}}%
%
\vskip0pt%
}

\makeatletter

\defbeamertemplate*{title page}{mydefault}[1][]
{
\vbox{}
\vfill
\begin{centering}

{\usebeamercolor[fg]{titlegraphic}\inserttitlegraphic\par}
\begin{beamercolorbox}[sep=8pt,center,#1]{title}
\usebeamerfont{title}\inserttitle\par%
\ifx\insertsubtitle\@empty%
\else%
\vskip0.25em%
{\usebeamerfont{subtitle}\usebeamercolor[fg]{subtitle}\insertsubtitle\par}%
\fi%
\end{beamercolorbox}%

\vskip1em\par

\begin{beamercolorbox}[sep=8pt,center,#1]{author}
\usebeamerfont{author}\insertauthor
\end{beamercolorbox}

\begin{beamercolorbox}[sep=8pt,center,#1]{institute}
\usebeamerfont{institute}\insertinstitute
\end{beamercolorbox}

\begin{beamercolorbox}[sep=8pt,center,#1]{date}
\usebeamerfont{date}\insertdate
\end{beamercolorbox}\vskip0.5em

\end{centering}
\vfill
}
%
\makeatother

\AtBeginSection[]{
\setbeamercolor{section in toc}{fg=black}
\setbeamercolor{subsection in toc}{fg=black}
\frame<beamer>{
\begin{multicols}{2}
\frametitle{\textbf{\insertshorttitle}}
\setcounter{tocdepth}{2}
\tableofcontents[currentsection,subsections]
\end{multicols}
}
}

\titlegraphic{\includegraphics[height=2.0cm]{./Basic_Fig/BUU_EN.jpg}}
%
\title[\textbf{ABCD (ABCDEFG)}]{\textbf{000000 ABCD}}
\subtitle{\textbf{ABCDEFG}}

\author{\textbf{AAAAA (BBBBBB)}}
\institute{\textbf{CCCCCCCC}}

\date{\textbf{XXXXX   YYYYY}}

\begin{document}
%
\begin{frame}[t]
\frametitle{\textbf{LaTeX – A document preparation system)}}
%
\begin{columns}[t]
%
\column{0.85\textwidth}
%
\begin{block}{\textbf{LaTeX}}
%
\textbf{
\begin{enumerate}
%
\itemLaTeX the product\\
•LaTeX is a high-quality typesetting system; it includes features designed for the production of technical and scientific documentation. LaTeX is the de facto standard for the communication and publication of scientific documents. LaTeX is available as free software.\\
•LaTeX is a high-quality typesetting system; it includes features designed for the production of technical and scientific documentation. LaTeX is the de facto standard for the communication and publication of scientific documents. LaTeX is available as free software.\\
%
\itemLaTeX the product\\
•LaTeX is a high-quality typesetting system; it includes features designed for the production of technical and scientific documentation. LaTeX is the de facto standard for the communication and publication of scientific documents. LaTeX is available as free software.\\
•LaTeX is a high-quality typesetting system; it includes features designed for the production of technical and scientific documentation. LaTeX is the de facto standard for the communication and publication of scientific documents. LaTeX is available as free software.\\
%
\end{enumerate}
}
%
\end{block}
%
\end{columns}
%
\end{frame}
%
%
\end{document}


-
Try adding \addtobeamertemplate{block begin}{\vspace{-25pt}}{} in your preamble. –  karlkoeller Jul 30 '13 at 5:43

It looks like columns environment introduces some vertical shift. In your example, columns is used to define block width. You can get same results with minipage environments which don't shift the block. Next code (I've suppressed titlepage and AtBeginSection fragments) shows results with columns and minipage.

\documentclass[compress,serif,xcolor=dvipsnames,xetex,t]{beamer}

\definecolor{Setcolor}{HTML}{6698FF}
\usecolortheme[named=Setcolor]{structure}

\usepackage{xltxtra}
\XeTeXlinebreaklocale "th"
\defaultfontfeatures{Scale=1.4}
\renewcommand{\baselinestretch}{1.35}
%\setmainfont[Script=Thai]{DilleniaUPC}

\usepackage[all,knot,color]{xy}
\xyoption{arc}
\usepackage{url}

{
\leavevmode%
\hbox{%
\end{beamercolorbox}%
\end{beamercolorbox}}%
\vskip0pt%
}

\setbeamertemplate{footline}
{
\leavevmode%
\hbox{%
\end{beamercolorbox}%
\end{beamercolorbox}%
\end{beamercolorbox}}%
\vskip0pt%
}

%

\title[\textbf{ABCD (ABCDEFG)}]{\textbf{000000 ABCD}}
\subtitle{\textbf{ABCDEFG}}

\author{\textbf{AAAAA (BBBBBB)}}
\institute{\textbf{CCCCCCCC}}

\date{\textbf{XXXXX   YYYYY}}

\begin{document}
%
\begin{frame}[t]
\frametitle{\textbf{Frame with \texttt{columns}}}
%
\begin{columns}[t]
%
\column{0.85\textwidth}
%
\begin{block}{\textbf{\LaTeX}}
%
\textbf{
\begin{enumerate}
%
\item \LaTeX\ the product\\
• \LaTeX\ is a high-quality typesetting system; it includes features designed for the production of technical and scientific documentation. \LaTeX\ is the de facto standard for the communication and publication of scientific documents. \LaTeX\ is available as free software.\\
%
\end{enumerate}
}
%
\end{block}
%
\end{columns}
%
\end{frame}
%

\begin{frame}[t]
\frametitle{\textbf{Frame with \texttt{minipage}}}
%
\centering
\begin{minipage}{.85\textwidth}
\begin{block}{\textbf{\LaTeX}}
%
\textbf{
\begin{enumerate}
%
\item \LaTeX\ the product\\
• \LaTeX\ is a high-quality typesetting system; it includes features designed for the production of technical and scientific documentation. \LaTeX\ is the de facto standard for the communication and publication of scientific documents. \LaTeX\ is available as free software.\\
%
\end{enumerate}
}
%
\end{block}
%
\end{minipage}
%
\end{frame}
%
\end{document}


-