As the most important ecosystem service function of the Three-River Source region, water conservation is the strategic support for promoting the ecological environment protection and high-quality development of this area. Based on the water production module in the InVEST model, combined with the shadow engineering method, we analyzed the temporal and spatial changes of the water conservation value of the Three-River Source region. We also used the coupling degree model to explore the coupling relationship between the regional conservation value and its influencing factors. The results showed that: (1) The water conservation value of the Three River region showed an overall upward trend from 1981 to 2020, with an average value of 156.207 billion yuan. The spatial distribution characteristics were more in the southeast and less in the northwest. The unit water conservation value of each region was as follows: source of Lancang River > source of Yellow River > source of Yangtze River. (2) There was a positive correlation between precipitation and water conservation value in each period. Before 2010, the correlation between precipitation and water conservation value was significant. After 2010, the correlation was not significant. The response of water conservation value to precipitation decreased. (3) The unit water conservation value of forest land and grassland was higher than the regional average, and the unit water conservation value of cultivated land, construction land and unused land was lower. The increase in the area of forest and grassland and the decrease in the area of unused land were important factors for the increase in the water conservation value of the Three-River Source region. (4) The per capita water conservation value of the Three-River Source region fluctuated, with an average value of 250200 yuan per person for this period; the regional economy of the Three-River Source region was developing rapidly, and the GDP growth rate was significantly higher than the growth rate of the water source conservation value. The ratio of the water source conservation value to GDP dropped from 15.48 to 2.89, the value multiplier of water conservation decreased significantly, and the scarcity of water conservation increased. (5) The coupling degree between the value of water conservation and various elements changed from being on the verge of imbalance to the primary coupling state, and the interaction gradually became stronger. As the uncertainty of future climate change increase, especially the rising temperature, it would become the main factor limiting the water conservation value of this region; promoting the transformation of unused land into ecological land would promote the steady improvement of the regional ecological environment quality. In addition, the Three-River Source region should focus on protecting natural resources and the ecological environment, changing the past production mode dominated by animal husbandry, and expanding the common development of multiple industries.