Modular multilevel converter(MMC) based on voltage sensor multiplexing is beneficial to reduce equipment cost and communication burden, however, usually leading to the performance degradation due to low estimation accuracy of the submodule capacitor voltage(SM-CV). This paper proposes a compensation method based on voltage sensor multiplexing for SM-CV estimation accuracy to solve this issue. In order to improve the estimation accuracy, the novel compensation methods of switching voltage drop and sampling deviation are proposed. The estimation accuracy of SM-CV is significantly improved by correcting the output voltage of the multiplexing group, and compensating for the sampling deviation of the corresponding submodule by modeling the error of the matrix equation Ax=b. Simulation results verify the feasibility of the proposed methods.