Objectives: Continuous renal replacement therapy (CRRT) plays a crucial role in critically ill patients with acute kidney injury (AKI). However, the predictive value of urine output (UO) for long-term prognosis after CRRT discontinuation is not fully understood. Methods: This retrospective study included AKI patients undergoing CRRT at three tertiary hospitals. Patients were categorized into four groups based on 24-hour UO at the time of CRRT discontinuation. All-cause mortality and the development of end-stage kidney disease (ESKD) one year after CRRT discontinuation were analyzed. Results: Among 852 patients, 61.4% were male, the mean age was 63.7 ± 16.0 years. During one year after CRRT discontinuation, 334 (39.2%) of 852 patients died, and 150 (30.1%) of 499 patients were diagnosed with ESKD. Multivariable analysis revealed that UO <1500 ml/day was associated with a higher risk for all-cause mortality (UO <100 ml/day: hazard ratio (HR) 3.06, 95% confidence interval (CI) 2.22–4.22; P < 0.01, UO 100–499.9 ml/day: HR 2.23, 95% CI 1.57–3.16; P < 0.01, UO 500–1499.9 ml/day: HR 1.70, 95% CI 1.18–2.44; P = 0.01), and for the development of ESKD (UO <100 ml/day: odd ratio (OR) 16.17, 95% CI 7.67–34.09; P < 0.01, UO 100–499.9 ml/day: OR 7.50, 95% CI 3.48–16.18; P < 0.01, UO 500–1499.9 ml/day: OR 3.40, 95% CI 1.54–7.48; P < 0.01) after adjusting for confounding variables. UO was negatively associated with the risk of ESKD, irrespective of diuretics use. Conclusions: This study underscores the importance of monitoring UO in predicting long-term risks of ESKD and mortality in critically ill AKI patients undergoing CRRT.