Polyphenylene sulfide (PPS) is a high-performance semi-crystalline thermoplastic polymer that is widely used in the automotive, electronics, and aerospace industries, as well as other fields. However, PPS introduces several challenges in fused deposition modeling owing to its inherent properties of crystallization and thermal crosslinking. The present study demonstrates the effects of the thermal processing and heat treatment conditions on the accuracy and mechanical properties of PPS samples three-dimensionally printed through fused deposition modeling. By measuring the degree of crystallinity and thermal crosslinking of three-dimensionally printed PPS samples, we found that the thermal history affects the three-dimensionally printed PPS properties. Results show that the accuracy of three-dimensionally printed PPS samples can be improved by means of air-forced cooling in fused deposition modeling. The balance between mechanical strength and ductility was regulated by altering the heat treatment conditions. This approach is applicable to eliminating the warpage of semi-crystalline polymer in three-dimensional printing (not only for PPS) and provides a method of improving the mechanical properties of three-dimensionally printed PPS samples.