Water conservation plays an important role in the ecological function of ecological public welfare forests. The water conservation capacity of ecological public welfare forests may be affected by the natural endowment of forests and forest management practices. One of the important goals of the collective forest rights system reform is to maintain ecological security. What changes have taken place in the water conservation capacity of ecological public welfare forests after the reform of the collective forest rights system? Does the reform have an impact on the change of water conservation capacity of ecological public welfare forests? In order to clarify these issues, this paper firstly analyzed the impacts of natural factors including forest land quality, forest species and precipitation, and social factors including the ownership of forest rights on the water conservation capacity of ecological public welfare forests from a theoretical perspective. Secondly, the comprehensive water storage capacity method was used to calculate and analyze the changes in the water conservation capacity of ecological public welfare forests before and after the collective forest rights system reform in 723 villages in 5 counties (districts) in Fujian Province. Finally, the multiple linear regression model was used to find out the key influencing factors of the reform of the collective forest rights system on the change of the ecological public welfare forest water conservation capacity. The results showed that: (1) after the reform of the collective forest rights system, the water conservation capacity of ecological public welfare forests generally increased in 5 counties (districts), but the water conservation capacity per unit area of ecological public welfare forests declined in 3 counties (districts) and increased in 2 counties (districts). (2) The ownership of ecological public welfare forests had a significant impact on the water conservation capacity per unit area through the management and protection of ecological public welfare forests. State-owned ownership had a positive effect on the water conservation capacity per unit area, and collective ownership and private ownership had a negative impact on the water conservation capacity per unit area. (3) Forest natural endowment factors such as area, proportion of planted forests, proportion of shelterbelts, changes in volume and rainfall, etc., had a significant impact on water conservation capacity per unit area mainly through forest resource structure, forest management conditions and forest external environment. Based on the above results, the following policy recommendations are proposed: (1) the management department of ecological public welfare forests cannot only focus on the increase of the quantity of ecological public welfare forests, but also pay attention to the quality improvement of ecological public welfare forests. (2) The government can appropriately increase the redemption of collective and privately owned ecological public welfare forests. (3) The operators of ecological public welfare forests can focus on tapping the potential of water conservation capacity of young artificial origin ecological public welfare forests, and protect the natural origin ecological public welfare forests and shelter forests.