Based on geological research on different regions of South China, different types of mineral deposits and different kinds of production mine enterprises from 1988 to 2016, the author tentatively discusses some key problems concerning deep exploration of mineral resources in such aspects as the target, the theory, the depth, the extent and the efficiency. Under the current technical and economic conditions, the author puts forward some suggestions:firstly, considering the national goal, scientific objectives and personnel, it is necessary to be flexible in the use of various metallogenic theories, to fully use the "Five levels+Basement" exploration model, and to take the potential bedded orebody and layered ore-bearing geological body as the main target in deep exploration of mineral resources. Secondly, according to the principle'from the known to the unknown and from the shallow to the deep', it is necessary to work in the mining areas especially in the orefields and/or ore concentration areas with relatively high degree of shallow geological work and relatively clear understanding of metallogeny, which can reduce the risk and can meet the practical needs. Thirdly, it is necessary to adhere to the principle that the 2000 m, 3000 m 5000 m deep drilling should be deployed in ore deposits, orefields and ore-concentration areas which have the highest degree of favorable geology and prospect so as to achieve the purpose of exploration. Fourthly, it is necessary to adhere to the principle of comprehensive evaluation, comprehensive survey, comprehensive evaluation and comprehensive study, paying attention to the reasonable probing depth and seizing key problem of deep exploration, so as to avoid the rash advance based on single subject of rash. Only in this way can good results be achieved.