High-speed surface-mounted permanent magnet synchronous machine is often used in micro gas turbine generation system due to its high rotor strength and high efficiency. The electrical machine in this kind of generation system needs to integrate two functions of starter and generator. Therefore, its comprehensive performance, including starting performance and generating performance, has become a comprehensive standard to measure machine performance. In this paper, a 40 kW, 20,000 r/min high-speed machine is taken as an example, the influence of magnets magnetization direction on the machine comprehensive performance is studied. The machine models with different magnets magnetization directions are established by using finite element method and the correctness of the models is verified by comparing the experimental data with the finite element calculation data. On this basis, the influence of different magnetization directions on the performance of the machine, such as generation loss, torque ripple, output voltage, start-up time and maximum starting ability, is analyzed. Furthermore, based on the Fourier decomposition of air gap flux density and the decoupling analysis of starting torque, the influence mechanism of magnetization direction on the performance of the machine is revealed. The presented results provide a reference for the selection of a suitable magnetization direction for high-speed surface-mounted permanent magnet machines.