Endometriosis is one of the common gynecologic diseases in women of reproductive age. The most common clinical symptoms include dysmenorrhea, dyspareunia, and chronic pelvic pain. Diagnostic laparoscopy is considered the gold standard for the diagnosis of endometriosis. However, it is an invasive and expensive procedure for clinical practice, and therefore endometriosis is usually diagnosed based on clinical symptoms, sonography, and serum CA-125. In recent years, Traditional chinese Medicine (TCM) has been widely used for the treatment of endometriosis, but evidence-based studies on its efficacy remain insufficient. In this study, we collected data on 146 endometriosis patients who underwent TCM treatment from Chang Gung Research Database (CGRD) and analyzed the prescriptions. The most common formulas are Gui-zhi-fu-ling-wan, Jia-wei-xiao-yao-san, and Long-dan-xie-gan-tang, and the most common single herbs are Pu-gong-ying (Herba Taraxaci), Xiang-fu (Rhizoma Cyperi), and Yan-hu-suo (Rhizoma Corydalis). After TCM treatments, 68.2% of patients with elevated serum CA-125 level had their level decreased (p < 0.01), and 78.8% of patients with normal serum CA-125 level had their level remained normal. As a result, we assumed that TCMs have potential effects on the treatment of endometriosis via regulating blood, rectifying qi, clearing heat, and invigorating qi. However, further studies are needed to prove the efficacy of these botanical drugs.