In this work, we propose a new configuration of surface plasmon resonance (SPR) sensor that is based on graphene–MoS2 hybrid structures for ultrasensitive detection of molecules. The proposed system displays a phase-sensitivity enhancement factor of more than 500-fold when compared to the SPR sensing scheme without the graphene–MoS2 coating or with only graphene coating. Our hypothesis is that the monolayer MoS2 has a much higher optical absorption efficiency (∼5%) than that of the graphene layer (∼2.3%). Based on our findings, the electron energy loss of MoS2 layer is comparable to that of graphene and this will allow a successful (∼100%) of light energy transfer to the graphene–MoS2 coated sensing substrate. Such process will lead to a significant enhancement of SPR signals. Our simulation shows that a quasi-dark point of the reflected light can be achieved under this condition and this has resulted in a steep phase jump at the resonance angle of our newly proposed SPR system. More importantly, we found that phase interrogation detection approach of the graphene–MoS2 hybrid structures-based sensing system is more sensitive than that of using the regularly angular interrogation method and our theoretical analysis indicates that 45 nm of Au film thickness and 3 coating layers of MoS2 nanosheet are the optimized parameters needed for the proposed SPR system to achieve the highest detection sensitivity range.