China is one of the typical countries with a wide range of karst landforms in the world, it has been a technical problem to build a dam under the geological conditions of karst development. The seepage analysis and control evaluation of the reservoir site plays an important role in the process of dam design and operation, and has an important impact on the safety of the rock mass and hydraulic structures in the reservoir site, as well as the economic rationality of reservoir operation. Here, a reservoir dam project under the geological condition of karst development was selected as the research object, combined with the engineering characteristics, a three-dimensional finite element model of seepage analysis was established based on the characteristics of the main dam structure and the hydrogeological conditions of the reservoir site. The saturated-unsaturated seepage calculation theory was used to calculate and analyze the seepage field in the reservoir site during the operation period. In addition, the seepage characteristics and change laws of the dam body, dam foundation and rock mass on both banks of the dam in the reservoir site were studied to evaluate the applicability of the anti-seepage system adopted in this project. The results show that the designed seepage control system in use can effectively reduce the groundwater level in the reservoir site, and the seepage gradient of each part of the reservoir site is generally small, which can meet the requirements of seepage stability. Moreover, under the effect of the current seepage control system, the leakage in the reservoir site is effectively controlled.