\documentclass[11pt, a4paper]{article}
\usepackage{chemfig}
\usepackage{xepersian}

\makeatletter
\@ifundefined{Umathcode}{\let\Umathcode\XeTeXmathcode}{}
\@ifundefined{Umathchardef}{\let\Umathchardef\XeTeXmathchardef}{}
\makeatother

\settextfont{Yas}
\begin{document}
 نمونه
\chemfig{H_2N-CO-N}

\lr{\chemfig{H_2N-CO-N}}
\end{document}