During the secondary thermoforming of carbon fiber-reinforced polyphenylene sulfide (CF/PPS) composites, a vital material for the aerospace field, varied thermal parameters profoundly influence the crystallization behavior of the PPS matrix. Notably, PPS exhibits a distinctive self-nucleation (SN) behavior during repeated thermal cycles. This behavior not only affects its crystallization but also impacts the processing and mechanical properties of PPS and CF/PPS composites. In this article, the effects of various parameters on the SN and non-isothermal crystallization behavior of PPS during two thermal cycles were systematically investigated by differential scanning calorimetry. It was found that the SN behavior was not affected by the cooling rate in the second thermal cycle. Furthermore, the lamellar annealing resulting from the heating process in both thermal cycles affected the temperature range for forming the special SN domain, because of the refined lamellar structure, and expelled various defects. Finally, this study indicated that to control the strong melt memory effect in the first thermal cycle, both the heating rate and processing melt temperature need to be controlled simultaneously. This work reveals that through collaborative control of these parameters, the crystalline morphology, crystallization temperature and crystallization rate in two thermal cycles are controlled. Furthermore, it presents a new perspective for controlling the crystallization behavior of the thermoplastic composite matrix during the secondary thermoforming process.