For the first time, a 3D stacking of MoS2 and Si CMOS integrated with embedded RRAM is proposed and fabricated, and CMOS inverter comprised of MoS2 nFET and Si pFET is demonstrated. Vertically stacked multiple MoS2 channels are required for the performance matching. Resistive switching (RS) of a Ti/MoS2 /p+-Si structure showing high ON/OFF ratio of 106 is demonstrated firstly by highly Si-compatible process. Surface modification is the key to formation of uniform and smooth stacked MoS2 multiple channels and to enhanced resistive switching endurance. This scheme can be applied to CMOS-based bipolar RRAM 1T1R or 2T1R without increasing the cell size. Our work offers a new pathway with high feasibility of integrated 2D materials and Si FETs into CMOS to enabling 3D embedded logics and memories for future computing systems.