Constructing a nature reserve system is important to realize China’s ecological civilization. However, scenic spots and nature reserves within the nature reserves system generally have the problem of overlapping in space, and there is no unified and effective solution in technology. By analyzing the differences in theoretical cognition and current technical practice between scenic spots and nature reserves, it is clear that the difference in resource value is the root cause of the overlapping problem. An analytical framework is proposed to unify the value context of ecosystem services and maximize service efficiency. The technical route of cross-conflict areas is adjusted by combining ecosystem service trade-offs and collaborative relationship classification. Taking Jinci-Tianlongshan Scenic Spot and Nature Reserve in Shanxi Province as an example, the ecosystem service value method was used to evaluate regional cultural services and support services. The Geoda model was used to analyze the correlation between the two types of services and land use patterns and the trade-offs and synergies between services. Combined with the relevant specifications of scenic spots, the evaluation of scenic resources, the evaluation of ecological sensitivity, and the analysis of the integrity of watershed units are carried out. Then, according to the above-mentioned results of weighing collaborative zoning, the intersection area’s adjustment intention and zoning optimization suggestions are preliminarily determined. Finally, the boundary range of scenic spots is determined by combining the administrative boundary, the three areas and three lines, the boundary of returning farmland to forest, the boundary of cultural relics protection, and the boundary of mining development. The zoning scheme aims at the optimal efficiency of ecosystem services and solves the problem of conservation conflicts caused by overlapping natural protected areas. This study can provide a reference for integrating and optimizing overlapping natural protected areas.