As one of the hot subjects in the world, biochemistry can help humans to understand and explore the geological and geochemical processes on the earth with new theories and methods, which have a significant impact on the research and application in the field of resources and environment. “Three- type Rare Resources” biological methods of prospecting for minerals include geobotany (visual examination of the vegetation cover), biogeochemistry (chemical analysis of vegetation), geozoology and microbial prospecting. Based on the summarization of previous academic research achievements combining with this study, the theory of “Three- type Rare Resources” biological methods for mineral exploration and its application significance have been further stated in this paper. Some successful cases show that “Three- type Rare Resources” biological methods of prospecting for minerals could be effectively applied to prospect concealed Li and Be rare metal ore deposits under covers. With the deepening and development of research, “Three- type Rare Resources” biological methods of prospecting for minerals might play a more important role on the development of theory and technology for the Three- type Rare Mineral Resources survey in China.