Abstract: Regional ecology and landscape are becoming increasingly fragmented in the context of global urbanization. The existing protected area system is difficult to ensure the comprehensive protection of the regional ecosystems due to administrative boundary restrictions. Aiming at the goal of integrating and optimizing regional protected areas, this research constructs a landscape character assessment method, which comprises the two stages of landscape character identification and ecological integrity assessment, to provide a basis for achieving the integrity protection of regional ecosystems. Taking the Huangshui Valley in Qinghai Province as an example, it carries out the landscape character assessment to obtain the background information on landscape character types, areas, and conservation priorities. The landscape character area is used as the basic spatial unit to guide the integration and optimization of protected areas in the Huangshui Valley. In particular, the integration and optimization process of the protected area system of the Daban Mountain system was highlighted.