According to the complexity of watershed management and the comprehensive characteristics of the goal of happy rivers and lakes construction, this paper combines the holistic governance theory with the construction of happy rivers and lakes in the Yellow River Basin, expounds the conceptual connotation of happy rivers and lakes, explores the compatibility of the holistic governance theory with happy rivers and lakes construction, and summarizes the current situation of happy rivers and lakes construction in the Yellow River Basin. Based on the perspective of holistic governance, this paper analyzes the practical problems in the happy rivers and lakes construction in the Yellow River Basin. The results show that there are still some problems in the Yellow River Basin, such as the contradiction between supply and demand of water resources is prominent, the relationship between water and sediment is not coordinated, the water environment and water ecological situation is severe, and the information construction is not perfect. Therefore, it is necessary to adhere to overall planning, optimize the allocation and utilization of water resources, improve comprehensive management, promote coordinated regulation of water and sediment, adhere to systematic governance, give full play to the joint efforts of multiple subjects, and strengthen digital enabling, accelerate the co-construction and sharing of information, so as to promote the construction process of happy rivers and lakes in the Yellow River Basin and realize the harmonious coexistence between human and nature.