The purpose of this paper is the design, analysis, and optimization of a new structure of a permanent magnet vernier machine (PMVM) with a high torque density and low rotor losses. First, the modulation principle and topology of this PMVM is introduced. Then, its average torque and rotor loss are enhanced and reduced by optimizing the flux modulation poles distribution. For the sake of further reducing the rotor losses on the premise of maintaining the torque density, the contribution of the air gap flux density harmonics to the rotor loss is analyzed. Then, a new topological structure of a rotor with a flux barrier is introduced to reduce the rotor losses due to the decrease of each harmful harmonic. Through the analysis of the structure of the PMVM with the flux barrier, the influence of the parameters on the performance is built. After that, a multi-objective optimization algorithm is used to optimize the PMVM so as to obtain the optimal performance. Moreover, the electromagnetic performance comparison between the newly proposed machine and the original one is presented to indicate that lower rotor losses can be obtained by the proposed machine when the torque is ensured. Finally, a prototype of proposed PMVM is built and further tested to verify the validities of the theoretical and finite-element analyses.