The invention relates to the technical field of deep prospecting of geological exploration, and provides a skarn type iron-rich ore deep exploration method and system based on multi-element geophysics, the method combines direct prospecting with indirect prospecting, adopts multiple geophysical methods such as gravity, magnetic method, electrical method, earthquake and the like, exerts the advantages of each geophysical method, and improves the exploration efficiency. According to the method, cross constraint and joint interpretation of multi-element geophysical information are carried out, deep ore body extension is deduced, drilling verification is carried out, geophysical well logging is carried out, geophysical interpretation results are repeatedly corrected with drilling and well logging information as constraints, accurate positioning of the hidden magnetite body is achieved, the exploration success rate is increased, and the exploration cost is reduced.