Under the background of Xi Jinping Thought on the Rule of Law requiring the "system, integrity and coordination" of accelerating law-based governance in China, the realization of the national strategic goal of ecological protection and high-quality development in the Yellow River Basin needs to embed the overall system view into the proposition of legal guarantee of the ecological environment in the Yellow River Basin, to shape the integralist thinking paradigm consistent of the Yellow River Basin ecological rule of law discourse system and standard order. Taking the overall system view as the analysis tool, the legal approach of ecological protection in the Yellow River Basin has three core issues: problem orientation, theoretical traceability and logical orientation.In the former, a"rational" system is unfinished, an "administrative order-control" law enforcement mechanism is leaky and a "risk prevention" dynamic response basin judicial security system is absent. In the middle, the modern rule of law is a specific unity integrating time, ideas and norms. The basic law of the legal structure of ecological protection in the Yellow River Basin should be carried out along the unity of vertical commonness and diachronic, the interaction of internal professionalism and power doctrine, and the integration of external public and private laws. In the latter, in order to achieve the goal of "good law and good governance" in the ecological protection of the Yellow River Basin, it is advisable to build an ecological protection legal system with both shape and spirit, an ecological protection law enforcement system of the Yellow River Basin that "combines the carrot and the stick" and establish an ecological protection judicial system in the Yellow River basin that "combines prevention and control".