\documentclass{book}
\usepackage{xepersian}
\defpersianfont\nastaligh[Scale=1.3]{IranNastaliq}
\makeatletter
\newcommand\mycustomfont[1]{\def\@mycustomfont{#1}}
  \renewcommand\section{\@startsection {section}{1}{\z@}%
                                   {-3.5ex \@plus -1ex \@minus -.2ex}%
                                   {2.3ex \@plus.2ex}%
                                   {\@mycustomfont\Large\bfseries}}
\renewcommand\subsection{\@startsection{subsection}{2}{\z@}%
                                     {-3.25ex\@plus -1ex \@minus -.2ex}%
                                     {1.5ex \@plus .2ex}%
                                     {\@mycustomfont\large\bfseries}}
\makeatother
\mycustomfont{\nastaligh}
\begin{document}
\chapter{مقدمه}
\section{پیدایش مسئله}
\subsection{از کجا شروع شد}
مقداری متن معمولی
\end{document}