Green exploration is the only choice to achieve both resource and ecological protection. With the application of shallow drilling technology to geological mapping in thin overburden of the desert steppe in Middle-East Inner Mongolia, a shallow drilling technical system based on green exploration has been preliminarily summarized in this paper, including combination of portable drilling equipment and tools, environment-friendly drilling fluid, drilling and well logging together; replacing trenching with drilling; construction organization and management. Meanwhile, some insufficiencies with the system has also been discussed. The system will contribute to the development of green exploration technology.