The dq current transformation method can be used to achieve the drive control of the maglev permanent magnet synchronous linear motor (MPMSLM). Specifically, the control of the suspension force Fz can be achieved by controlling the d-axis current, and the control of the thrust force Fx can be achieved by controlling the q-axis current. However, the direct use of the dq current transformation method on traditional MPMSLM structures produces an additional rotation torque around the y-axis. In order to reduce this additional torque, a new MPMSLM structure is proposed in this work. First, the characteristics of additional torque through finite element analysis are analyzed. Second, the Halbach permanent magnet array and coil size are optimized, and the topology of the MPMSLM coil is designed to reduce the additional torque. The decoupling performance and current of the proposed MPMSLM are experimentally verified through open-loop experiments using finite element simulation software. Finally, the decoupling algorithm of the generalized inverse matrix is used to achieve the decoupling between forces Fx and Fz and torque Ty and the d-axis and q-axis currents in each drive unit. Based on this, a three-degree-of-freedom closed-loop control system of the MPMSLM is designed. The LabVIEW 2018 software is used for the simulation analysis of the three-degree-of-freedom MPMSLM motion control system, and the results show that the proposed motor structure has superior closed-loop control performance.