The invention provides a granite stratum division comparison method. The method comprises the following steps: 1, preparing logging curve data; 2, analyzing logging curve maximum entropy spectrum; 3, obtaining a data difference curve; 4, converting the data difference curve into a frequency spectrum curve; 5, performing filtering processing on a reconstructed frequency spectrum curve; 6, determining abnormal points; 7, numbering the abnormal points; and 8, performing stratum division and comparison: connecting key similar difference points of each well on a backbone profile according to a sequence, i.e., finishing granite stratum division comparison. According to the invention, the abnormal points in each well are analyzed and compared, compared to a conventional similar stratum comparison method, for a granite stratum which is small in lithologic difference, small in vertical change and not obvious in cyclicity, the operability is higher, and compared to a conventional stratum comparison method, the practicality is higher. Since a maximum entropy spectrum analysis method is employed, the stratum comparison quantitative degree is enhanced, the operability is higher, and the stratum comparison efficiency is greatly enhanced.