The association between surgical treatment for obstructive sleep apnea (OSA) in chronic kidney disease (CKD) patients and end-stage renal disease (ESRD) and survival outcomes is not established, and this study aimed to evaluate this association. A retrospective cohort analysis was conducted from 2001 to 2015, including 32,220 eligible CKD patients with incident OSA. By 1:3 propensity score matching, 1078 CKD patients with incident OSA who received surgery (treated cohort) and 3234 untreated cohort who never received surgery were analyzed. The risk of ESRD in the competing mortality was significantly lower in the treated cohort than in the untreated cohort, with an adjusted hazard ratio (aHR) of 0.38 (95% confidence interval (CI0, 0.15−0.97; p = 0.043). In addition, the adjusted HRs of overall, cardiovascular, and non-cardiovascular mortality in the treated and untreated cohorts were 2.54 (95% CI, 1.79−3.59; p < 0.0001), 1.46 (95% CI, 0.29−7.22; p = 0.64), and 2.62 (95% CI, 1.83−3.75; p < 0.0001), respectively. Furthermore, the risks of overall and non-cardiovascular mortality for the treated cohort primarily occurred during a 3-month follow-up. In conclusion, surgical treatment for incident OSA in CKD patients was associated with decreased ESRD risk, but with increased non-cardiovascular mortality risk, especially within 3 months after surgical treatment.