In order to explore the distribution law of crystal blockage in the drainage pipeline of the tunnel drainage system under the effect of groundwater seepage, the 1:5 tunnel drainage system indoor simulation test was established based on the Liaoshan Tunnel Project of the Ehan Expressway, and the same ionic composition test solution was prepared based on the analysis results of the on-site sampling groundwater to carry out the indoor test. The results show that: (1) The crystal stacking mode is mainly mass stacking, and the crystal structure type is irregular and square, belonging to isomerism crystal type, and the main component is calcite calcium carbonate; (2) With the increase of water flow, the crystallization amount increases and the crystallization rate becomes faster. The cumulative total crystallization reaches 106.4g under the condition of 266.8mL/s water flow at the lateral drainage outlet; (3) the gentle slope of the drainage pipe is conducive to the formation of crystals in the drainage pipe of the tunnel; (4) The total amount of crystallization at the joint of the drainage pipe (30%)>the total amount of crystallization at the horizontal drainage outlet (27%)>the total amount of crystallization at the horizontal drainage pipe (19%)>the total amount of crystallization at the longitudinal drainage pipe (15.2%)>the total amount of crystallization at the circumferential drainage pipe (8.3%). The key positions of crystal blockage in the tunnel drainage system are the interface of the drainage system and the outlet of the horizontal drainage pipe. The research results are helpful to the optimal design and construction quality control of the tunnel drainage system, and are of great significance to ensure the smooth and effective operation of the tunnel drainage system.