Green development is crucial to global natural resource conservation, environmental improvement and sustainable development. Furthermore, resource-based cities’ green development is more challenging compared with that of other types of cities. On such basis, it is a necessity to understand the green development level of such cities. Therefore, we introduce green development efficiency (GDE), which is a key indicator for measuring green development. This paper takes China’s 112 resource-based cities during 2010–2019 as its research object, and examines their GDE using the Super-SBM-Undesirable model. Moreover, industrial structure upgrading (ISU) and human capital structure upgrading (HCSU) have important implications for green development. To further explore the influence of ISU and HCSU on GDE, this paper employs a fixed effect model, an interaction effect model and a threshold model. Finally, considering the differences between different resource-based cities, the heterogeneity of ISU and HSCU on GDE in four types of China’s resource-based cities is also explored. It is found that (1) although GDE is on the track of steady improvement, the overall GDE was still relatively low during 2010–2019, with an average GDE of about 0.8; (2) ISU, HCSU and their interaction can promote GDE in resource-based cities and with the intensity of industrial structure increasing, the interaction effect of ISU and HSCU on GDE in resource-based cities shifts from positive to negative; (3) there exists heterogeneity in the direct effect and interaction effect of ISU and HCSU among four types of resource-based cities (i.e., mature cities, growing cities, declining cities and regenerating cities). Our findings offer a data reference for the green and sustainable development of China’s resource-based cities, and also a method reference for other countries’ resource-based cities.