Jiawei Foshou San (JFS) is the new formula originated from classic Foshou San formula, composed with ligustrazine, ferulic acid, and tetrahydropalmatine. Previously JFS inhibited the growth of endometriosis (EMS) with unclear mechanism, especially in metastasis, invasion, and epithelial–mesenchymal transition. In this study, network pharmacology was performed to explore potential mechanism of JFS on EMS. Through compound–compound target and compound target–EMS target networks, key targets were analyzed for pathway enrichment. MMP–TIMP were uncovered as one cluster of the core targets. Furthermore, autologous transplantation of EMS rat’s model were used to evaluate in vivo effect of JFS on invasion, metastasis and epithelial–mesenchymal transition. JFS significantly suppressed the growth, and reduced the volume of ectopic endometrium, with modification of pathologic structure. In-depth study, invasion and metastasis were restrained after treating with JFS through decreasing MMP-2 and MMP-9, increasing TIMP-1. Meanwhile, JFS promoted E-cadherin, and attenuated N-cadherin, Vimentin, Snail, Slug, ZEB1, ZEB2, Twist. In brief, anti-EMS effect of JFS might be related to the regulation of epithelial–mesenchymal transformation, thereby inhibition of invasion and metastasis. These findings reveal the potential mechanism of JFS on EMS and the benefit for further evaluation.