Permanent magnet synchronous machines provide many dramatic electromagnetic performances such as high efficiency and high power density, which make them more competitive in aircraft electrification, whereas, designing a permanent magnet starter–generator (PMSG), with given consideration to fault tolerance (FT), is a significant challenge and requires great effort. In this paper, a comprehensive FT PMSG design process is proposed which is applied to power systems of turboprops. Firstly, potential slot/pole combinations were selected based on winding factor, harmonic losses and manufacture issues. Then, pursuing high power density, a multiple objective optimization process was carried out to comprehensively rank performances. To meet a fault tolerance target, electrical, magnetic and thermal isolation topologies were investigated and compared, among which 18 slot/12 pole with dual three-phase was selected as the optimal one, with a power density of 7.9 kW/kg. Finally, a finite element analysis verified the performance in normal and post-fault scenarios. The candidate machine has merits concerning high power density and post-fault performance.