In a method for in-situ U-Pb dating of heterogeneous minerals, a target mineral is separated and purified by carrying out data analysis, extraction and enhancement on original mapping data. The method highlights distribution features of dating indexes (U content, Pb content, Pb206/U238 ratio, Pb207/U235 ratio and Th/U ratio) in a target mineral phase with a noise data processing technology, and more intuitively displays a favorable dating portion and a crystal growth change trend of the dating mineral. Further, a fine spot design is provided for high-precision dating analysis in a later stage. A plurality of geological events experienced by a heterogeneous mineral crystal in a growth process is accurately limited, so as to invert the mineral formation history which provides the basis for better study of mineralogy, mineral geochemistry and mineral geochronology. It is hence a novel indispensable auxiliary means of mineral geochronology and an auxiliary method for mineral exploration.