To complete groundwater diversion, the complex flow law of groundwater in rocks must be investigated so that groundwater diversion can be improved. This research uses the computer finite element method (FEM), CT scanning calculation method, Avizo method, and digital core technology combined with the Fluent calculation method (FCM) to reconstruct rocks with microscopic pore structures on a computer. The numerical simulation results under different conditions show that: the total pressure change gradually decreases under different pressure gradients. In a seepage channel, the seepage path does not change with the change in seepage pressure, and the seepage velocity is the largest in the center of the pore. The longer the seepage path is, the greater the decrease in seepage velocity. Different seepage directions have similar seepage laws. The research results provide effective guidance for the project to control groundwater.