The evolution and spatial distribution of fractures are key factors in the sealability of mudstone caprock. To investigate the evolution of crack initiation, propagation, coalescence during the process of deformation and failure for mudstone, uniaxial compression test and real-time CT scanning have been carried out for mudstone specimens of Longmaxi Formation. The crack evolution under different load levels is discussed; and the relationship between crack evolution and macroscopic deformation is revealed from the mesoscopic scale based on the variations of crack area and fractal characteristics of crack structure. The results show that: the evolution of mudstone cracks can be reflected with the changes of grey frequency and crack area. When the load applied on the specimen is at a level of 0-20%, even though crack area increases rapidly, crack initiation is not active due to the closing effect of cracks in compression process. When the load reaches a level of 20%-65%, crack area changes little owing to the generating effect and closing effect of cracks contributing equally; thus mudstone is in a stable stage. When the load is up to a level of 65%-85%, crack area increases sharply as the uniaxial effect of crack extension and coalescence speeds up. The sudden increase of crack area at the load level of 65% exhibits the burstiness and instantaneity of crack transformation from initiation, closing to extension. The complicated and disordered internal structures and cracks evolving from specimen surface to interior are clearly observed with the further increase of load. The curve of crack fractal dimension appears the “up―down―up―down” trend, which shows the evolution of initiation, closure, extension and coalescence of cracks.