The minimal supersymmetric extension of the standard model (MSSM) is extended to the $U(1)_X$SSM, whose local gauge group is $SU(3)_C \times SU(2)_L \times U(1)_Y \times U(1)_X$. To obtain the $U(1)_X$SSM, we add the new superfields to the MSSM, namely: three Higgs singlets $\hat{\eta},~\hat{\bar{\eta}},~\hat{S}$ and right-handed neutrinos $\hat{\nu}_i$. The CP violating effects are considered to study the lepton electric dipole moment(EDM) in $U(1)_X$SSM. The CP violating phases in $U(1)_X$SSM are more than those in the standard model(SM). In this model, some new parameters $(\theta_S, \theta_{BB^{\prime}}, \theta_{BL})$ as CP violating phases are considered, so there are new contributions to lepton EDMs. It is conducive to exploring the source of CP violation and probing new physical beyond SM. Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. Article funded by SCOAP3 and published under licence by Chinese Physical Society and the Institute of High Energy Physics of the Chinese Academy of Science and the Institute of Modern Physics of the Chinese Academy of Sciences and IOP Publishing Ltd.