The purpose of this paper is to reveal the relationship between the suction, discharge flow control and self-designed co-rotating scroll hydrogen circulation pump (CSHCP) aerodynamic performance and irreversible flow loss. The effect of five suction angles and five discharge spoiler positions on the performance and flow loss of a CSHCP was firstly revealed using the computational fluid dynamics (CFD) three-dimensional numerical simulation method combined with entropy production (EP) theory and omega vortex identification methods. The optimized suction angle and discharge spoiler position of CSHCP were identified through comparing with isentropic and volumetric efficiency, EP, vortex distribution and flow pulsation intensity. Subsequently, the performance and flow loss difference of CSHCP are further distinguished before and after optimization of suction and discharge spoiler structure under designed or variable rotational velocities. The results demonstrate that the optimized suction angle and discharge spoiler position angle are 22.5° and 45°, respectively. After the combination optimization of suction and discharge spoiler structure, the total EP and discharge temperature pulsation intensity of CSHCP are reduced by about 13.2% and 67.5% respectively. The research results provide a reference for the efficient and stable operation of HCP for fuel cell system.