The Natural Forest Protection Project (NFPP) is an ecological restoration project aimed at safeguarding natural forests, and is one of China’s six main forestry initiatives. The upper reaches of the Yangtze River represent the main distribution area of natural forests in China, and are an important area for the implementation of the NFPP. A systematic assessment of forest ecosystem changes in the upper Yangtze River region before and after implementation of the NFPP is of great scientific significance for the improvement of the project implementation effect, regional ecological protection, and further protection and restoration of natural forest resources. This study uses the NFPP area in the Yangtze River’s upper reaches as the study area; the data are primarily derived from the 1998 and 2020 forest resources category II survey data, long-term monitoring data from forest ecological stations, and public social data published by authoritative Chinese organizations. Based on the above data, we used the full index system of forest ecosystem services, continuous observation, and inventory system with the distributed measurement method to analyze the dynamic changes in forest ecosystem services in the study area in terms of three aspects: physical quality, value quality, and dominant function. The results of the study show that: (1) over the studied time scale, compared to the 1998 baseline, the physical quantities (soil erosion control, water regulation, and PM10 retention) and value of each service function of the forest ecosystem in the upper reaches of the Yangtze River project area in 2020 showed a significant increasing trend; (2) at the spatial scale, changes in forest ecosystem service functions in the upper reaches of Yangtze River under the NFPP showed significant spatial heterogeneity from 1998 to 2020; (3) in 2020, the total value of forest ecosystem services in the study area was 3,261,161,000,000 yuan/a, of which the functional value of biodiversity conservation was 1,294,426,000,000 yuan/a and the functional value of water conservation was 841,069,000,000 yuan/a, indicating that the forest ecosystem of the study area plays an important role as a “green gene pool” and “green water reservoir”; (4) the forest ecosystem service functions of the NFPP in the upper reaches of Yangtze River are intricately tied to forest resource features such as forest area, forest volume, age-group structure of arbor forest, etc., which influence the physical quantity and value of each forest ecosystem service function to varying degrees. In addition to illustrating the amazing efficiency of the natural forest preservation initiative, this study provides a scientific foundation for future natural forest resource conservation and restoration. It can serve as a reference for the project’s subsequent development as well to provide scientific foundations and guidance for the development of the natural forest protection and restoration program and to promote the protection and restoration of more natural forest resources.