The integrated geophysical and geochemical prospecting methods are faced with challenge from complex geological condition, A single geophysical or geochemical analysis method is not persuasive, and hence the integration of various geological information and exploration methods is particularly important. The application of the integrated geophysical prospecting method system to a deposit in Henan Province is described in this paper based on practice. According to geological data and concrete geological facts, geophysical methods such as high precision magnetic survey, X-ray soil analysis and EH4 were used in an integrated way for concealed ore body prospecting. A clear geophysical and geochemical anomaly is related to metallization and matches well with geological phenomena, which suggests that the integrated geophysical and geochemical prospecting method system is effective in the molybdenum deposit, and it has the advantages of rapidity, efficiency and practicality.