Endometriosis is a common benign disease in women of reproductive age. It has been defined as a disorder characterized by inflammation, compromised immunity, hormone dependence, and neuroangiogenesis. Unfortunately, the mechanisms of endometriosis have not yet been fully elucidated, and available treatment methods are currently limited. The discovery of new therapeutic drugs and improvements in existing treatment schemes remain the focus of research initiatives. Chinese medicine can improve the symptoms associated with endometriosis. Many Chinese herbal medicines could exert antiendometriosis effects via comprehensive interactions with multiple targets. However, these interactions have not been defined. This study used association rule mining and systems pharmacology to discover a method by which potential antiendometriosis herbs can be investigated. We analyzed various combinations and mechanisms of action of medicinal herbs to establish molecular networks showing interactions with multiple targets. The results showed that endometriosis treatment in Chinese medicine is mainly based on methods of supplementation with blood-activating herbs and strengthening qi. Furthermore, we used network pharmacology to analyze the main herbs that facilitate the decoding of multiscale mechanisms of the herbal compounds. We found that Chinese medicine could affect the development of endometriosis by regulating inflammation, immunity, angiogenesis, and other clusters of processes identified by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The antiendometriosis effect of Chinese medicine occurs mainly through nervous system-associated pathways, such as the serotonergic synapse, the neurotrophin signaling pathway, and dopaminergic synapse, among others, to reduce pain. Chinese medicine could also regulate VEGF signaling, toll-like reporter signaling, NF-kappa B signaling, MAPK signaling, PI3K-Akt signaling, and the HIF-1 signaling pathway, among others. Synergies often exist in herb pairs and herbal prescriptions. In conclusion, we identified some important targets, target pairs, and regulatory networks, using bioinformatics and data mining. The combination of data mining and network pharmacology may offer an efficient method for drug discovery and development from herbal medicines.