Abstract: Since China has elevated the construction of ecological civilization to the level of a national development strategy, its theory and practice have profoundly reshaped the core elements of the traditional mineral resource development and protection governance structure, and promoted the dynamic transformation of the mineral resource development and protection governance structure. Based on the structuralist perspective and adopting the normative research method, this paper systematically analyzes the internal mechanism of the transformation of the governance structure of mineral resource development and protection under the background of ecological civilization construction. The transformation mechanism of the governance structure is mainly reflected in three aspects: firstly, the governance goal has shifted from simply pursuing economic GDP to pursuing green GDP, thus achieving an ecological transformation of governance goals. Secondly, governance affairs have shifted from specialized management to holistic governance, achieving a systematic transformation of governance affairs. Thirdly, the relationship between governance departments has shifted from a single dominant position to a multi-dominant position, the relationship between government departments has shifted from separation to mutual trust, the relationship between government and enterprises has shifted from collusion to cooperation, and the relationship between government and society has shifted from suspension to embedding. These elements constitute the governance framework for the development and protection of mineral resource, which aims to achieve sustainable utilization of mineral resources and long-term protection of the ecological environment. The overall transformation can be summarized as “green transformation”, the core of which includes ecological environmental protection, economic greening and relationship standardization, which together point to the ultimate form of mineral resource development and protection. From a micro level, it expands the theoretical boundaries of mineral resource development and protection governance, and provides a theoretical basis for coordinating mineral resource development and environmental protection. From a macro level, it provides practical inspiration for promoting the coordinated development of resource economy, ecological civilization construction and green transformation of economy and society, and also provides support for achieving the sustainable development goal of harmonious coexistence between man and nature.