Deep prospecting has always been difficult and ineffective. Logging as an important means of prospecting for metal ores has been used for many years, but its deep prospecting application is still in the exploration stage, and its effect also needs evaluation. In this paper, the authors took the mining borehole log data from the Fengyan-Xiekeng ore district of Meixian Town in Youxi County of Fujian Province as the research object by analysis of the tri-component magnetic survey, resistivity logging,and IP logging method application effect of deep prospecting in this area. Through the comparison of core observation and analysis, the identification effect of mineralization section and various logging response characteristics were analyzed comprehensively. It is thought that among several logging methods, the resistivity logging is relatively effective in search for lead-zinc deposits, whereas magnetic survey is effective for lead-zinc ore block with high ore grade. On the whole, the two kinds of logging methods are respectively effective to a certain extent, but their effects in search for deep molybdenum ares are not ideal, with no corresponding relationship. Based on a comprehensive analysis of the logging application for deep ore prospecting in this area, the authors hold that, for deep prospecting, researchers should analyze well logging application conditions. In the process of mineral exploration, a more effective means of logging detection should be used to find the corresponding relationship with mineralization, which can help reduce the blindness of regional prospecting work. In the borehole suitable for the exploration conditions, well logging is somewhat effective in the detection and prediction of deep orebody, determination of the attitude and the size of the orebody and locating of its spatial location. Generally, the logging method can play a supplementary role and can improve prospecting success rate.