Endometriosis (EM) is a chronic disease severely impacting reproductive health, with its exact cause still unclear. In-depth understanding of the etiology and pathogenesis of EM from the perspective of genetics and exploring individualized treatment strategies can improve the health and quality of life of patients. In this study, whole blood cis- expression quantitative trait loci (eQTL) data were used as exposure data, and data from the FinnGen database EM1-2 and EM3-4 were used as outcomes. Summary-data-based mendelian randomization (SMR) methods were used to select genes with causal relationship to the disease. These genes were validated through bioinformatics analysis and real-time quantitative polymerase chain reaction (RT-qPCR) analysis of clinical samples, and potential diagnostic and drug targets were screened through co-localization and molecular docking. Through SMR analysis, seven genes were selected as potential diagnostic markers of EM, namely Eukaryotic Elongation Factor, Selenocysteine-TRNA Specific (EEFSEC), INO80 complex subunit E (INO80E), RAP1 GTPase activating protein (RAP1GAP), Lipid Droplet Associated Hydrolase (LDAH), Ring Finger And SPRY Domain Containing 1 (RSPRY1), HLA Complex Group 22 (Non-Protein Coding) (HCG22) and Adenosine Kinase (ADK). Colocalization analysis showed that EEFSEC, HCG22, INO80E and RSPRY1 could be used as potential drug targets. The study identifies potential diagnostic markers and drug targets for EM from a genetic perspective, providing new directions for drug development and precision medicine for EM treatment.