The recycling of marine exploration equipment after it has surfaced is greatly affected by sea state. In order to estimate the sea state in real time, this paper proposes a method for measuring wave elevation, which modifies the integrated results of GNSS/SINS in the up direction by virtual horizontal lines to extract wave fluctuation information. From these wave information, the significant wave heights (SWH) can be calculated as the only input parameter of P-M spectrum, and a series of wave height data can be further simulated. When the GNSS is interrupted due to severe sea state, the simulated data can be integrated with the SINS to deal with the data distortion problem. The simulation results show that the application of wave spectrum in the GNSS intermittent situation has obvious improvement effect and important significance.