Aiming at the destruction of the ecological environment of the comprehensive geological structure, the traditional restoration countermeasures have the problems of high input cost and low economic benefits. For this reason, the ecological environment destruction process and restoration countermeasures of the comprehensive geological structure were proposed. The common geological structure characteristics and the impact of activities on the ecological environment in the mining area were analyzed. Based on the analysis results, an evaluation system for the degree of damage to the ecological environment by mining activities was constructed. According to the expert scoring method, a rating standard was developed to measure the degree of damage to the ecological environment. Depending on the degree of damage, appropriate recovery measures were formulated. The experimental results show that compared with the traditional restoration countermeasures, considering the destruction of the ecological environment during the mining process of comprehensive geological structures, the proposed restoration countermeasures have the advantages of low cost and high economic benefits.