As an important barrier to China’s ecological security, the Yellow River Basin has an irreplaceable strategic significance in the overall situation of national development and socialist modernization. Based on the national strategy of ecological protection and high-quality development of the Yellow River Basin, combined with the natural ecological characteristics and economic and social development of the Yellow River Basin, the comprehensive governance of the Yellow River Basin must adhere to collaborative governance. Under the theoretical framework of synergistic governance, public affairs governance covers five core dimensions: goal synergy, institutional synergy, subject synergy, factor synergy and regional economic development synergy. The governance of the Yellow River Basin needs to start from the above five dimensions to build a comprehensive governance system. In-depth analysis of the core problems facing the governance of the Yellow River Basin, it is proposed to build a comprehensive governance strategy by strengthening the policy and legal support system, reforming the management system, building a multi-dimensional co-management mechanism, optimizing the systematic governance system, and promoting the upstream, midstream and downstream synergistic development.