Introduction: Cattail Pollen is a commonly used Chinese medicine for promoting blood circulation and removing blood stasis in infertility patients with endometriosis, but its ingredients and mechanism of action are still unclear. The aims of this study were to explore the potential active ingredients, targets and mechanisms of Cattail Pollen in treating infertility patients with endometriosis based on bioinformatics and molecular docking. Methods: The GSE120103 dataset was downloaded from the Gene Expression Omnibus (GEO) database to screen out differentially expressed genes. Cytoscape software was constructed to construct the protein-protein interaction network and screen for hub proteins, and molecular docking was performed to identify the binding activity of Cattail Pollen active ingredients and infertility genes. Then, DAVID software was used to perform gene ontology (GO) functional analysis and KEGG pathway enrichment analysis on differentially expressed genes. Results: There were 1320 differentially expressed genes in patients with endometriosis. ADCY5, RLN3, and ADCY6 proteins encoded by genes that were upregulated in infertile patients with endometriosis. Eight active ingredients of Cattail Pollen were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform: naringenin ((2R)-5,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one), arachidonic acid, isorhamnetin, beta-sitosterol, kaempferol, Testosterone palmitate, kaempferol-3-O-alpha-L-rhamnosyl(1 -> 2)-beta-D-glucoside and quercetin. Molecular docking identified that the binding activity of arachidonic acid with ADCY5, RLN3, and ADCY6; and testosterone palmitate with ADCY5 and ADCY6 was strong. GO analysis suggested that differentially expressed genes were involved in multiple biological processes, cellular components, and molecular functions. KEGG enrichment analysis found that differentially expressed genes were enriched in neuroactive ligand-receptor interaction, cytokine-cytokine receptor interaction, chemokine signaling pathway, and Jak-STAT signaling pathway. Conclusions: This study discovered the differentially expressed genes of naturally conceived and infertile patients with endometriosis, and clarified the effective ingredients, targets, and potential signaling pathways of Cattail Pollen in the treatment of infertility patients with endometriosis.