In this study, we've analyzed some new gravity data obtained from two profiles across the Longmenshan (LMS) Fault system in order to determine the density structure and isostatic state of the crust beneath the Songpan–Ganzi block (SG) and the Sichuan basin (SC). According to our research, Bouguer gravity anomalies along the two profiles range from − 450 mGal in the SG to − 80 mGal in the SC. And density structural models show obvious differences between the SG and the SC. Compared with the SC, the SG has lower average density in the crust, and it has a low-density layer with thickness of 5 km in the middle crust. In the SC area, however, the crustal density increases gradually with depth and there exists no low-density layer in the crust. The Moho interface decreases from 60 km beneath the SG in east Tibet to 40 km beneath the SC. In the LMS region, the topography, Bouguer gravity, and Moho depth change abruptly in a narrow tectonic belt. The crustal isostatic state, which is derived from the Airy compensation model based on the topography, gravity and deep seismic sounding data, indicates that the SG on the northwest side of the LMS is not in an isostatic state, compared with the isostatic crust beneath the SC. The isostatic equilibrium of the crust under the northeast section of the LMS is not achieved as that in the southwest section of the LMS. Based on the research, we infer that the non-homogenous collision between the Tibetan Plateau and the Yangtze Craton has caused the strong variation of the Moho depth and the special isostatic state of the crust in this area.