In order to enhance performance of automotive suspension with embedded-permanent-magnet magnetorheological (MR) damper, V-model developing flow of electronic control unit was adopted to study control system of the suspension. First of all, rapid control prototyping (RCP) system of suspension with embedded-permanent-magnet MR damper was built up based on real-time simulation platform D2P; control algorithm of fruit fly optimization algorithm– proportional-integral-derivative was designed and experiments of RCP simulation were carried out. Moreover, model of suspension with embedded-permanent-magnet MR damper was built with the instruction of magnetic field composition theory. On these bases, hardware in the loop simulation (HILS) platform was built up and HILS experiments were carried out as well. Finally, bench tests were carried out, whose results, together with simulation results, indicated that the controlling system of suspension with embedded-permanent-magnets MR damper in the given research could enhance automobiles’ ride performance and the designed control strategy and algorithm were good.