\documentclass[12pt]{report}
\usepackage{amsthm,amsmath}
\usepackage{xepersian}
\settextfont{Yas}

\newtheorem{theorem}{قضیه}[section]

\renewcommand{\thetheorem}{%
  \ifnum\value{section}=0 
    \rl{\thechapter}% "no section"
  \else
    \rl{\thesection}% at least within a section
  \fi%
  .\arabic{theorem}}

\begin{document}

\chapter{فصل با بخش}
\section{بخش اول}
\begin{theorem}
سلام ~\ref{abc} و~\ref{def}.
\end{theorem}
\begin{theorem}\label{abc}
سلام
\end{theorem}
\section{بخش دوم}
\begin{theorem}
سلام
\end{theorem}
\begin{theorem}
سلام
\end{theorem}

\chapter{فصل بدون بخش}
\begin{theorem}\label{def}
سلام
\end{theorem}

\end{document}