The rotary energy recovery device (RERD) plays an important role in reverse osmosis (RO) desalination; however, few investigations on the formation and influence of lateral force on the RERD rotor have been published. The transient characteristics of lateral force and its relationship with pressure distribution and fluctuation in the clearance were analyzed via computational fluid dynamics (CFD) simulation. The clearance pressure distribution and lateral force were quantified under different working conditions. The eccentricity of the rotor, resistance torque and decrease in the rotary speed due to the lateral force were simulated and they were found to change with flow rate and pressure of high-pressure outlet (PHO). A new rotary speed prediction method including the effect of PHO was developed. With the increasing flow rate or PHO, the stability of RERD declined. A design optimization direction was proposed. The variation trends of rotary speed, pressure in the clearance and its fluctuation were verified through experiment. This research provides an explanation why in practice the rotary speed decreases with increasing pressure. The conclusions obtained herein can be of great significance for future research on improving the stability and lifespan and reducing the maintenance consumption of RERD.