Phase change material (PCM) as highly efficient temperature control material has been used in photovoltaic-thermoelectric (PV-TE) coupling system to achieve higher power generation efficiency. The periodic energy balance and PCM regeneration are the key factors that affect the temperature control effect and system total performance. In present paper, a numerical model for space PV-PCM-TE system was established with the composite of paraffin and aluminum foam as PCM. Firstly, the impact of periodic energy imbalance on PCM regeneration characteristics and system overall performance was investigated under space conditions. Then, to regulate the periodic energy transmission of the coupling system, a global structural parameters optimization was performed, and the optimal parameter combination was derived and validated, where porosity of aluminum foam, thickness of PCM layer, thermal concentration factor, length of TE legs, and surface area ratio are 0.94, 4.08 mm, 25.83, 1.09 mm and 1.80, respectively. The validation results show that after optimization, the periodic energy balance and PCM full utilization and regeneration can be achieved. The average total efficiency of optimal case is 30.72%, which is a little lower than that with the surface area ratio of 7.0 (31.77%), but the average power density is 49.64% higher. The present work validates that periodic energy balance design is important for space PV-PCM-TE system and the global parameter optimization method is an effective optimization method, which is significant for the design and optimization of PCM based temperature control system.