This paper aims to improve control performance for a magnetorheological damper (MRD)-based semi-active seat suspension system. The vibration of the suspension is isolated by controlling the stiffness of the MRD using a proportion integration differentiation (PID) controller. A new intelligent method for optimizing the PID parameters is proposed in this work. This new method appropriately incorporates particle swarm optimization (PSO) into the PID-parameter searching processing of an improved fruit fly optimization algorithm (IFOA). Thus, the PSO-IFOA method possesses better optimization ability than IFOA and is able to find a globally optimal PID-parameter set. The performance of the PID controller optimized by the proposed PSO-IFOA for attenuating the vibration of the MRD suspension was evaluated using a numerical model and an experimental platform. The results of both simulation and experimental analysis demonstrate that the proposed PSO-IFOA is able to optimize the PID parameters for controlling the MRD semi-active seat suspension. The control performance of the PSO-IFOA-based PID is superior to that of individual PSO-, FOA-, or IFOA-based methods.