The Yangtze River’s substantial variation in water depth and current speeds means that inland ships face diverse operational conditions within a single voyage. This paper discusses the adoption of controllable-pitch propellers, which adjust their pitch to adapt to varying navigational environments, thereby optimizing energy efficiency. We developed an optimization framework to determine the ideal pitch angle and rotation speed (RPM) under different sailing conditions. The energy performance model for inland ships was enhanced to account for the open-water efficiency of CPPs across various pitch angles and RPMs, considering the impacts of current and shallow water, among other factors. The optimization approach was refined by incorporating an improved genetic algorithm with an annealing algorithm to enhance the initial population, applying the K-means clustering algorithm for population segmentation, and using multi-parent crossover from diverse clusters. The efficacy of the optimization method for CPP operations was validated by analyzing three operational scenarios of a Yangtze sailing ship. Additionally, key components of the ship performance model were calibrated through experimental tests, demonstrating an anticipated fuel consumption reduction of approximately 5% compared to conventional fixed-pitch propellers.