Due to the asymmetry of charge distribution and geometric structure, the Janus membrane can simultaneously intercept counter-ions and co-ions. This work constructed four Janus membrane configurations using numerical simulation methods. Due to the different potential within the membrane and the selectivity level, there is a significant deviation in the interception performance. The results found that the change in the height of the Janus membrane affects the distribution of anion and cation concentration inside the nanochannel, and the asymmetry of the nanochannel height is more conducive to interception than a uniform nanochannel. The effect of the nanochannel length of the first section on the rejection rate is higher than that of the second section. Considering the design of the membrane, we recommend that the pore length of the first section be set to about 50 nm. Since the flow potential balances the electroviscous force, the optimization of the flow rate for ion transport is often opposite to the interception effect. The Janus membrane has asymmetric pore size and charge distribution characteristics and has excellent retention ability for divalent salts under low-pressure intensity and high-concentration conditions.