Improving green total factor productivity (GTFP) is a fundamental solution to help the strategic mineral industry to achieve green and sustainable development. This study incorporates the dual negative externalities of resource depletion and environmental pollution into the GTFP measurement to capture the ‘green’ elements. By employing a truncated third-order (TTO) translog cost function and the feasible generalized least squares (FGLS) approach, we evaluate the GTFP growth performance and its components in China’s strategic minerals industry from 1998 to 2017. Moreover, we explore the bias of technological progress toward the resource and environmental factors to grasp the green factor saving effects. The results show that: (1) during the sample period, the average GTFP growth rate of China’s strategic minerals industry was 0.46%, but there were variances between mineral sectors. Nevertheless, after 2012, the GTFP of all mineral sectors experienced different degrees of decrease. (2) The main driver of adjustments in GTFP growth shifted from technological progress to changes in scale efficiency, with technological progress contributing less to GTFP growth. This is particularly evident in the metal and energy minerals sectors. (3) Green technological progress is biased toward saving environmental factor input but enhancing resource extraction. Therefore, the current development of China’s strategic minerals industry falls into a non-sustainable mode of being environmentally friendly but not resource-saving.