<p>The changing environmental conditions and unique topographical features have created the complex and variable hydrological characteristics of karst basins, leading to practical issues such as the difficulty in coordinating flood control and beneficial use objectives and low water resource utilization efficiency for reservoirs in these basins. To improve the operation and management level of reservoirs in karst areas, this study constructs an optimal reservoir operation system under comprehensive coordination of the full operational cycle. The system integrates the division of the reservoir’s full operational cycle, the derivation of stage-specific design floods and adjustment of flood limit water levels, and multi-objective optimal operation of the reservoir, and is applied to the Chengbi River Reservoir in a typical karst basin in southwestern China. The results showed that the reservoir’s full operational cycle was divided into five periods: water supply, pre-flood, main flood, post-flood, and water storage. A three-dimensional Frank copula function was constructed using flood peak discharge, 1-day/3-day flood volumes to derive design floods under joint distribution, with adjusted flood limit levels of 185 m (pre-flood), 184.5 m (main flood), and 185–187.6 m (post-flood). Particle swarm optimization was used to solve daily/10-day scale optimization models for flood control-water supply-power generation, showing increased power generation and end-of-operation storage in wet/normal/dry years compared to actual operations. The research findings hold significant theoretical and applied values for improving the comprehensive utilization of water resources and the operation management level of reservoirs in karst regions.</p>