The invention discloses a granite microscopic crack structure identification and microscopic seepage analysis method. The method comprises the following steps: reading a granite monopolarization microscopic image M; sequentially carrying out super-pixelated segmentation and filtering processing on the granite monopolarized microscopic image M to obtain a granite microscopic digital image M2; performing binarization processing on the granite microscopic digital image M2 to obtain a granite microscopic binarization image M3; analyzing to obtain a fluid flow velocity distribution map, a fluid pressure distribution map and equivalent permeability of the granite microcrack system; analyzing and obtaining a fluid flow velocity profile and a fluid pressure profile in the granite microcrack system-granite matrix system. The method is practical, simple and low in cost, the granite monopolarization microscopic image M can be repeatedly utilized, visual research is conducted on the seepage law ofthe granite microcrack system, and the equivalent permeability of the granite microcrack system can be easily calculated.