In order to adapt to the construction of ecological civilization and the “two in one” responsibilities of natural resources departments, plus the relevant informatization deployment of the Ministry of Natural Resources, we absorb and summarize the existing informatization experience, and put forward a natural resource data governance system construction idea that meets the actual needs of the administrative departments of natural resources, including the construction of a natural resources data standard specification system, a three-dimensional natural resources “one map” big data system, a space-business-temporal relationship, a distributed data management mechanism, and an update and maintenance mechanism. On the basis of the data governance system, the application direction of in-depth mining, analysis and prediction of natural resources big data is discussed to assist natural resources regulatory decision-making. Finally, a case of using the big data center of the land space basic information platform to support the construction and operation of the natural resource data governance system is introduced.