Large surface and underwater vehicles are typically equipped with two sets of Rotational Inertial Navigation Systems (RINS), which operate independently following the same rotation modulation strategy. The systems only serve as mutual backups, lacking effective information fusion. To improve RINS accuracy, a joint rotation modulation scheme based on sensors information fusion is proposed under the configuration of two RINSs. The classic single axis rotation scheme is optimized at first without changing the structure and arrangement of any single RINS. The rotational strategies and start-stop sequences of the Inertial Measurement Units (IMUs) of both systems are jointly designed to ensure that at any given moment, one RINS is in a stationary state. The output information (from the gyroscopes and accelerometers) of the IMUs during the stationary phases is fused in sequence to reduce the coupling effect between IMU rotation, scale factor errors, and installation errors. Theoretical analysis of error characteristics verifies the advantages of the proposed modulation scheme. Simulation results show that the position error of the system using the joint rotational modulation scheme has decreased from 2.3 n mile/72 h of a single normal RINS to 0.7 n mile/72 h under the typical sensor level.