The Ping-Chong-Jiang-Ni Formula (PCJNF), a compound of Traditional Chinese Medicine (TCM), has demonstrated remarkable clinical effectiveness and is widely utilized in the treatment of endometriosis (EMs). Previous studies have shown that PCJNF inhibits the proliferation and induces the apoptosis of ectopic endometrial stromal cells (EESCs) by modulating the JNK signaling pathway. In our most recent study, published in January 2024, we found that PCJNF effectively alleviates EMs-associated pain by reducing inflammatory mediators, including tumor necrosis factor-alpha (TNF-α) and nerve growth factor (NGF). Furthermore, PCJNF down-regulates the expression of transient receptor potential vanilloid 1 (TRPV1), phosphorylated TRPV1 (p-TRPV1), and protein kinase C (PKC). To further investigate the therapeutic potential of PCJNF, we conducted a comprehensive tandem mass tag (TMT) proteomics analysis, identifying 4984 proteins co-expressed in human EESCs treated with PCJNF and control serum. Based on these findings, this study explored the inhibitory effects of PCJNF on the migration and invasion of EMs cells in vitro. Reverse transcription-polymerase chain reaction (RT-PCR) analysis of 12 genes revealed a significant upregulation of FER and TRIP13 in ectopic lesions, which was further validated by immunohistochemistry. Given the crucial role of TRIP13 in EMs, we employed small interfering RNA (siRNA) to knock down its expression, observing a marked reduction in the migration and invasion abilities of EMs cells. Conversely, overexpression of TRIP13 using short hairpin RNA (shRNA) enhanced these processes. Additionally, after PCJNF treatment, we observed significant alterations in the expression of migration-and invasion-related proteins, such as vimentin and E-cadherin. In conclusion, these findings suggest that TRIP13 may serve as a potential therapeutic target for EMs and that PCJNF offers a promising new approach for integrating Traditional Chinese Medicine with modern medical treatments.