Nature reserves in the Yellow River Basin are important ecological barriers in China. They play an important role in protecting biodiversity，preserving natural heritage，improving ecological environment quality and maintaining national ecological security. For the nature reserves across administrative regions in the Yellow River Basin，the current compartmentalized administrative management system is not conducive to the realization of multiple interests of nature reserves，while the inter-governmental cooperation system can make up for this deficiency. Within the existing legal framework，the implementation of inter-governmental cooperation mechanism of nature reserves in the Yellow River Basin needs to be strengthened. From the perspective of law，the inter-governmental cooperation system of cross-administrative nature reserves in the Yellow River Basin consists of three parts：decision-making，implementation and supervision of the implementation mechanism；internal coordination and external coordination of the rule of law coordination mechanism；information sharing and dispute resolution of security mechanism. The construction of these mechanisms needs to be combined with the basic theories of constitution and administrative law to promote the realization of the protection interests of nature reserves.