Introduction: We aimed to identify different trajectories of fluid balance (FB) and investigate the effect of FB trajectories on clinical outcomes in intensive care unit (ICU) patients with acute kidney injury (AKI) and the dose-response association between fluid overload (FO) and mortality. Methods: We derived data from the Beijing Acute Kidney Injury Trial (BAKIT). A total of 1,529 critically ill patients with AKI were included. The primary outcome was 28-day mortality, and hospital mortality, ICU mortality and AKI stage were the secondary outcomes. A group-based trajectory model was used to identify the trajectory of FB during the first 7 days. Multivariable logistic regression was performed to examine the relationship between FB trajectories and clinical outcomes. A logistic regression model with restricted cubic splines was used to examine the dose relationship between FO and 28-day mortality. Results: Three distinct trajectories of FB were identified: low FB (1,316, 86.1%), decreasing FB (120, 7.8%), and high FB (93, 6.1%). Compared with low FB, high FB was associated with increased 28-day mortality (odds ratio [OR] 1.94, 95% confidence interval [CI] 1.17–3.19) and AKI stage (OR 2.04, 95% CI 1.23–3.37), whereas decreasing FB was associated with a reduction in 28-day mortality by approximately half (OR 0.53, 95% CI 0.32–0.87). Similar results were found for the outcomes of ICU mortality and hospital mortality. We observed a J-shaped relationship between maximum FO and 28-day mortality, with the lowest risk at a maximum FO of 2.8% L/kg. Conclusion: Different trajectories of FB in critically ill patients with AKI were associated with clinical outcomes. An FB above or below a certain range was associated with an increased risk of mortality. Further studies should explore this relationship and search for the optimal fluid management strategies for critically ill patients with AKI.