The invention discloses a deep prospecting prediction method for a hydrothermal vein type tin-tungsten polymetallic ore deposit, which comprises the following steps of: on the basis of carrying out large-scale structure-alteration lithofacies fine analysis and typical rock and ore control structure mechanical property identification on different middle section key sections in a mining area, combining isotope chronology and fluid inclusion geochemistry; through cooperation with verification of geophysical prospecting means such as wide-area electromagnetism and ground high-precision magnetic measurement, the purposes of finding out fracture mechanical transformation characteristics and ore control effects of tin-tungsten ore bodies and lead-zinc ore bodies, revealing the relation between the two ore control fractures, deducing characteristics of deep structure bonding zones, dividing ore control structure systems of mining areas and improving the ore control effect are achieved. And summarizing a structural ore control rule and an alteration zoning rule of the ore deposit, delineating an alteration rock geochemical anomaly region, proposing a deep favorable prospecting section, and finally establishing a prospecting model. According to the method, a basis is provided for prediction and exploration of the deep-edge hidden ore body of the mine.