<p>Alternative splicing (AS) plays a crucial role in various diseases, yet its functional significance in endometriosis remains poorly understood. In this study, we analyzed RNA-seq data from 146 endometriosis patients and 114 control endometrial samples (normal endometrium) to investigate aberrant AS events (AASEs) in endometriosis. Transcriptome profiling identified 1,005,616 transcripts, including 379,829 reference, 418,431 novel, and 207,356 intergenic transcripts, highlighting extensive transcriptomic diversity. A total of 91,767 alternative splicing events (ASEs) were detected, of which 4,850 were classified as AASEs. GO enrichment analysis showed that AASE-associated genes were significantly enriched in biological processes such as “regulation of small GTPase-mediated signal transduction” and “regulation of protein localization to plasma membrane,” which may contribute to disease progression by modulating cell proliferation, invasion, and adhesion. By correlating the expression of differentially expressed RNA-binding proteins (RBPs) with the percent spliced in (PSI) values of ASEs, we constructed a regulatory network comprising 20 RBPs and 644 AASEs, revealing potential post-transcriptional regulatory mechanisms. Additionally, splicing quantitative trait locus (sQTL) analysis identified 26,430 sQTLs associated with 29,654 ASEs. Notably, several high-confidence sQTLs were located within known endometriosis-associated genes, including androgen receptor (AR) and grainyhead like transcription factor 2 (<i>GRHL2</i>). Together, these findings provide new insights into the molecular mechanisms of endometriosis from the perspective of AS regulation.</p>