In order to meet the requirement of industrial production, a control system of a novel flux reversal linear rotary permanent magnet actuator (FR-LRPMA) is developed in this paper, and the electromagnetic and motion decoupled process is analyzed in detail. Firstly, the control equation of FR-LRPMA is derived in the nine phase stator coordinate system and dual dq-axis mover coordinate system. Then the control model of FR-LRPMA is built in MATLAB/Simulink using improved space vector pulse width modulation (SVPWM), and the linear, rotary and spiral motions of the proposed actuator are achieved. Finally, the prototype of the actuator is manufactured, and the experiment platform of FR-LRPMA is set up to measure the cogging torque and linear detent force, validating the simulation results. It is concluded that the control system of FR-LRPMA can be converted into two independent single freedom motors by dual dq transformation. The improved SVPWM is effective in the control system, and the method can be used to solve the electromagnetic and motion decoupling problems.