Abstract: Natural forests and public welfare forests play crucial roles in national ecological security and sustainable economic and social development. At present, China’s natural forests and public welfare forests share consistent primary functions and exhibit a high degree of spatial overlap, leading to the continuous advancement of integrated management for both. In light of the current management status of natural forests and public welfare forests in Yunnan province, this article systematically summarizes the achievements since the implementation of integrated management, analyzes existing issues, and puts forward relevant suggestions. The aim is to provide references for establishing a unified management system, improving the dynamic adjustment mechanism for compensation and subsidies, and achieving “one map, one set of data, one management system, one guiding plan, and one evaluation standard” for natural forest protection and public welfare forest management. This article will promote the sustained and healthy development of public welfare forest ecosystems, with natural forests as the main component.