Natural resources, as the material basis of human life and production, play a crucial role in national economic and social development. It is essential to reveal the structural characteristics of global natural resource supply and demand, which has become one of the most critical factors affecting every country’s policy strategy and economic development. However, mining the characteristics of international natural resource trades is a huge challenge because of the availability and quality of trade data. In this study, the international natural resource trade system is modeled as networks based on the available bilateral trade data from 2000 to 2016. Complex network methods and spatial analysis are utilized to explore the networked and spatial characteristics of different international natural resource trade networks (INRTNs). First, we quantitatively present the overall evolution trend of INRTNs by calculating several indicators of network features at the macrolevel. Then, as the intermediate-level characteristics of INRTNs, the core–periphery structures are explored by applying hierarchical clustering and a visual matrix heatmap. Finally, at the microlevel, the imbalance in direction is detected through the combination of node importance in a complex network with bivariate choropleth maps of spatial analysis. The empirical evidence from INRTNs of different product types in this paper will help governments and business administrations to perceive the complex natural resource trade environment, which can instruct policymakers to formulate effective import–export policies and ensure national resource security and sustainable development.