Water seepage in grotto relics, i.e., Yungang Grottoes, Dazu Rock Carvings, is a key issue to accurately describe the deterioration and weathering process of grotto rock mass. Considering rainfall infiltration, Finite element simulation was performed for studying the water flow through macro-channel of fractured rock in the 4th cave of Yungang Grottoes, where a group of joints with directions of S62°E and N5°W are widely developed. A 3D atom-based representative model was derived from X-ray diffraction (XRD) patterns and the related semi-quantitative calculation of grotto rock powders, for visualizing the associated seepage characteristics through micro-channel by means of molecular dynamics simulation, for the first time. By analyzing various properties, ranging from the configuration and energetic behaviors to the dynamic characteristics, the calculated water flux and mass flow rate were equal to 270 ns−1 and 8.10 × 10–12 g s−1, respectively. A dynamic process of water transport from the entrance region to the exit region was examined and it is consistent with the relative concentration profiles at the corresponding stage. The tagged O atoms experienced a zigzag movement instead of linear motion as expected, roughly exhibited the same target direction. The seepage characteristics in grotto relics experienced a complex evolution process and three types can be summarized: water infiltrates through micro-channels with a low flow rate; it flows through fracture with a relatively high flow rate; it turned into a kind of analogous pipe flow in inter-connected fracture network, resulting in water seepage hazard. Current simulation studies provide helpful insights for understanding the water flow-infiltration behavior of fractured rock in grotto relics.