1You can define subfigures:
2
3\begin{pandoccrossrefsubfigures}
4
5\subfloat[1]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig1.png}\label{fig:subfig1}}
6\subfloat[2]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig2.png}\label{fig:subfig2}}
7\subfloat[3]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig3.png}}
8
9\subfloat[4]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig4.png}\label{fig:subfig4}}
10\subfloat[5]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig5.png}}
11\subfloat[6]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig6.png}\label{fig:subfig6}}
12
13\subfloat[7]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig7.png}\label{fig:subfig7}}
14\subfloat[8]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig8.png}}
15\subfloat[9]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig9.png}\label{fig:subfig9}}
16
17\caption[{Caption}]{Caption}
18
19\label{fig:subfigures}
20
21\end{pandoccrossrefsubfigures}
22
23\begin{pandoccrossrefsubfigures}
24
25\subfloat[1]{\includegraphics{fig1.png}\label{fig:subfig21}}
26
27\subfloat[2]{\includegraphics{fig2.png}\label{fig:subfig22}}
28
29\subfloat[3]{\includegraphics{fig3.png}}
30
31\subfloat[4]{\includegraphics{fig4.png}\label{fig:subfig24}}
32
33\subfloat[5]{\includegraphics{fig5.png}}
34
35\subfloat[6]{\includegraphics{fig6.png}\label{fig:subfig26}}
36
37\subfloat[7]{\includegraphics{fig7.png}\label{fig:subfig27}}
38
39\subfloat[8]{\includegraphics{fig8.png}}
40
41\subfloat[9]{\includegraphics{fig9.png}\label{fig:subfig29}}
42
43\caption[{Caption}]{Caption}
44
45\label{fig:subfigures2}
46
47\end{pandoccrossrefsubfigures}
48
49Figures themselves can be referenced fig.~\ref{fig:subfigures2}, as well
50as individual subfigures:
51figs.~\ref{fig:subfig1}, \ref{fig:subfig2}, \ref{fig:subfig29}
52