According to the Chinese president XI Jin-ping's idea of ecological civilization construction in the New Era and the concept of "mountain, river, forest, farmland, lake and grassland are a life community", and in the context of the concept, connotation and attribute analysis of the natural resources, the hierarchical classification scheme of the natural resources serving the comprehensive investigation work, eight basic categories of underground space, minerals, shallow geological layer, land, water, forest, grassland and wetland, and its space-time and attribute structures were established. Based on these works, the comprehensive investigation system frame of natural resources that follows the basic flow of unified basic investigation, special thematic investigation, dynamic monitoring and data update, data processing and comprehensive integration, results expression and application services, has been primarily built. Besides, the work content and the requirement of each stage have been briefly discussed, which provides a reference for reconstruction of natural resources comprehensive investigation system.