\documentclass[12pt,a4paper,fleqn]{article}{...}
\usepackage{amsthm,amssymb,amsmath}
\usepackage{xepersian}
\settextfont[Scale=1.1]{XB Niloofar}
\numberwithin{equation}{section}
\begin{document}
\begin{flushleft}
\begin{equation}
\begin{aligned}
y_{1}^{.}=\beta_{1}(y_{2}-y_{1})+u_{1} \\
y_{2}^{.}=(\beta_{2}-\beta_{1})y_{1}-y_{1}y_{3}+\beta_{2}y_{2}+u_{2}\\
y_{3}^{.}=y_{1}y_{2}-\beta_{3}y_{3}+u_{3} 
\end{aligned}
\end{equation}
\end{flushleft}




\end{document}