\documentclass{jarticle}
\usepackage{graphicx}

\newlength{\subfigwidth}
\newlength{\subfigcolsep}
\setlength{\subfigcolsep}{2\tabcolsep}
\setkeys{Gin}{width=\subfigwidth}

\makeatletter 
\renewcommand{\thefigure}{% 
\thesection.\arabic{figure}} 
\@addtoreset{figure}{section} 
\makeatother 

\usepackage{subfigure}

\begin{document}

\section{A}

参照すると、図\ref{fig:figa01}、図\ref{fig:figa11}、図\ref{fig:figa12}、
図\ref{fig:figa21}、図\ref{fig:figa22}、図\ref{fig:figa31}、図\ref{fig:figa32}
となります。

\begin{figure}
  \setlength{\subfigwidth}{.5\linewidth}
  \addtolength{\subfigwidth}{-.5\subfigcolsep}
  \begin{minipage}[b]{\subfigwidth}
    \centering\subfigure[The first one.]{\includegraphics[width=3cm]{tiger.eps}
   \label{fig:figa11}}
  \end{minipage}
  \begin{minipage}[b]{\subfigwidth}
    \centering\subfigure[The second one.]{\includegraphics[width=3cm]{tiger.eps}
   \label{fig:figa12}}
  \end{minipage}
  \begin{minipage}[b]{\subfigwidth}
    \centering\subfigure[The third one.]{\includegraphics[width=3cm]{tiger.eps}
   \label{fig:figa21}}
  \end{minipage}
  \begin{minipage}[b]{\subfigwidth}
    \centering\subfigure[The fourth one.]{\includegraphics[width=3cm]{tiger.eps}
   \label{fig:figa22}}
  \end{minipage}
  \begin{minipage}[b]{\subfigwidth}
    \centering\subfigure[The fifth one.]{\includegraphics[width=3cm]{tiger.eps}
   \label{fig:figa31}}
  \end{minipage}
  \begin{minipage}[b]{\subfigwidth}
    \centering\subfigure[The sixth one.]{\includegraphics[width=3cm]{tiger.eps}
   \label{fig:figa32}}
  \end{minipage}
  \caption{subfigures.}
  \label{fig:figa01}
\end{figure}

\newpage

参照すると、図\ref{fig:figb00}、図\ref{fig:figb01}、図\ref{fig:figb02}、
図\ref{fig:figb03}、図\ref{fig:figb04}、図\ref{fig:figb05}、図\ref{fig:figb06}
となります。

\begin{figure}
  \setlength{\subfigwidth}{.5\linewidth}
  \addtolength{\subfigwidth}{-.5\subfigcolsep}
  \begin{minipage}[b]{\subfigwidth}
    \centering\subfigure[The first one.]{\includegraphics[width=3cm]{tiger.eps}
    \label{fig:figb01}}
  \end{minipage}
  \begin{minipage}[b]{\subfigwidth}
    \setcounter{subfigure}{3}
    \centering\subfigure[The fourth one.]{\includegraphics[width=3cm]{tiger.eps}
    \label{fig:figb04}}
  \end{minipage}
  \begin{minipage}[b]{\subfigwidth}
    \setcounter{subfigure}{1}
    \centering\subfigure[The second one.]{\includegraphics[width=3cm]{tiger.eps}
    \label{fig:figb02}}
  \end{minipage}
  \begin{minipage}[b]{\subfigwidth}
    \setcounter{subfigure}{4}
    \centering\subfigure[The fifth one.]{\includegraphics[width=3cm]{tiger.eps}
    \label{fig:figb05}}
  \end{minipage}
  \begin{minipage}[b]{\subfigwidth}
    \setcounter{subfigure}{2}
    \centering\subfigure[The third one.]{\includegraphics[width=3cm]{tiger.eps}
    \label{fig:figb03}}
  \end{minipage}
  \begin{minipage}[b]{\subfigwidth}
    \setcounter{subfigure}{5}
    \centering\subfigure[The sixth one.]{\includegraphics[width=3cm]{tiger.eps}
     \label{fig:figb06}}
  \end{minipage}
  \caption{Up-down ordering of the subfigures.}
  \label{fig:figb00}
\end{figure}

\end{document}
