To explore the correlation between the levels of serum complement C1q/ tumor necrosis factor associated protein 3 (CTRP3) and solitary G protein coupled receptor ligand (Apelin) of patients with endometriosis (EMS) and their dysmenorrhea degree and infertility. Methods: A total of 305 patients with endometriosis from May 2019 to May 2022 were selected in study group retrospectively, and 260 healthy women with the similar age during the same period were selected in control group. The serum CTRP3 and Apelin levels of the patients were detected by enzyme-linked immunosorbent assay. Spearman correlation was used to investigate the relationship between the serum CTRP3 and Apelin levels of the patients with endometriosis and their degree of dysmenorrhea. Receiver operating characteristic (ROC) curve was used to evaluate the predictive value of the serum CTRP3 and Apelin levels of the patients with endometriosis for their infertility. Results: The serum CTRP3 level (256.6±72.7 ng/ml) of the patients in the study group was significantly lower than that (465.6±50.4 ng/ml) of the patients in the control group, and the serum Apelin level (4.5±2.0μg/L) of the patients was significantly higher than that (2.0±0.4μg/L) of the patients in the control group. With the aggravating of dysmenorrhea of the patients with EMS, the serum CTRP3 level had decreased gradually and the serum Apelin level had increased gradually. The serum CTRP3 level of the patients with infertility was significantly lower than that of the patients without infertility, and the Apelin level of the patients with infertility was significantly higher (all P<0.05). Spearman correlation analysis showed that serum CTRP3 level of the patients with EMS was negatively correlated with their dysmenorrhea, and the serum Apelin level of the patients with EMS was positively correlated with dysmenorrhea (P<0.05). ROC curve analysis showed that the area under the curve of the serum CTRP3 level and the Apelin level of the patients for predicting their EMS and infertility were 0.864 and 0.755, the cut-off value of which were 240.4ng/ml and 4.0μg/L, the sensitivity of which were 92.3% and 92.3%, and the specificity of which were was 66.4% and 57.1%. The area under the curve, the sensitivity, and the specificity of the combined levels of serum CTRP3 and Apelin of the patients for predicting their EMS and infertility were 0.905, 86.6%, and 85.5%, respectively. Conclusion: The serum CTRP3 level of the patients with EMS decreases and the Apelin level of the patients with EMS increases, and both the levels of CTRP3 and Apelinare of the patients are closely related to their dysmenorrhea degree, and which are expected to be the effective indicators for predicting the infertility and EMS of the patients.