همه \nonumberها رو پاک کنین و بعدش از محیط split استفاده کنین:
\documentclass{article}
\usepackage{amsmath}
\begin{document}
\begin{align}\label{Eq}
\begin{split}
&\left( {\begin{array}{*{20}{c}}
{{d_1}}&{{d_2}}\\
{{d_3}}&{{d_4}}
\end{array}} \right)\left\{ \begin{array}{l}
A\\
B
\end{array}
\right\} = - {\omega ^2}{X_b}\left\{ \begin{array}{l}
{F_1}\\
{F_2}
\end{array} \right\}\\[3mm]
&\left[ D \right] = \left( {\begin{array}{*{20}{c}}
{{d_1}}&{{d_2}}\\
{{d_3}}&{{d_4}}
\end{array}} \right)\\[3.3mm]
&{d_1} = - {M_1}{\omega ^2} + {C_1}i\omega + {K_1}\\[3mm]
&{d_2} = {K_c} + {C_2}i\omega \\[3mm]
&{d_3} = {K_c} + {C_3}i\omega \\[3mm]
&{d_4} = - {M_2}{\omega ^2} + {C_4}i\omega + {K_2} + \frac{{i\omega \,v{c_2}^2}}{{c{p_2}\,i\omega \, + \,\frac{1}{{R{l_2}}}}}\\[3mm]
&{F_1} = - \int_0^L {{m_1}} \phi (x){\mkern 1mu} dx - M{t_1}{\mkern 1mu} \phi (L)\\[3.3mm]
&{F_2} = - \int_0^L {{m_2}} \psi (x)dx - M{t_2}\psi (L)
\end{split}
\end{align}
\end{document}
