The establishment of a protected area system network at the watershed scale is conducive to the overall protection of fragmented habitat patches，and provides a safe ecological base for the green development of watershed territory space. This study systematically combed the necessity，existing problems and key challenges of the protected area system network construction at the watershed scale，and proposes the principles and main methodology for planning the protected area system network. Taking the Yangtze River Economic Belt as the study area，a protected area system network with network core patches，connecting corridors，and important small patches as the core elements was systematically constructed，which may provide a reference for the overall protection of important ecosystems at the watershed scale.