$U(1)_X$SSM is a non-universal Abelian extension of the Minimal Supersymmetric Standard Model (MSSM) and its local gauge group is
extended to $SU(3)_C\times SU(2)_L \times U(1)_Y\times U(1)_X$. Based on the latest data of neutral meson mixing and experimental limitations, we investigate the process of $B^{0}-\bar{B^{0}}$ mixing in $U(1)_X$SSM. Using the effective Hamiltonian method, the Wilson coefficients and mass difference $\triangle m_{B}$ are derived. The abundant numerical results verify that $~v_S,~M^2_D,~\lambda_C,~{\mu},~M_2,~\tan{\beta},~g_{YX},~M_1$ and $~\lambda_H$ are sensitive parameters to the process of $B^{0}-\bar{B^{0}}$ mixing. With further measurement in the experiment, the parameter space of the $U(1)_X$SSM will be further constrained during the mixing process of $B^{0}-\bar{B^{0}}$.