The convergence management is needed for the times to deepen the reform of the ecological civilization system. Since the institutional reform of the State Council in 2018, the comprehensive management of natural resources has been strengthened, but there is still some problems of management disconverge, which greatly affects the management efficiency. Based on the problem-oriented approach, this paper analyzes the problems, such as unintegration of concepts, uncoordinated systems, uncoordinated systems, inconsistent standards, and data without sharing. Based on the systematic and holistic view, this paper proposes suggestions for the natural resource integration management mechanism from five aspects: strengthening concept recognition, enhancing system linkage, exploring decision-making innovation, optimizing department responsibilities, and advancing technological convergence.