Crystallization-induced blockages in tunnel drainage systems pose significant challenges to their functionality and longevity. To address this issue, this study proposes a novel adaptive drainage pipe designed to prevent crystallization. By constructing an indoor experimental model for anti-crystallization tests, combined with scanning electron microscopy (SEM) and molecular dynamics simulations, this study investigates the mechanism and effectiveness of the proposed system. The findings reveal that flexible PVC pipes in dynamic flow and expansion states significantly reduce crystallization compared to conventional PVC pipes. Among tested materials, EVA and TPU demonstrate superior crystallization resistance, with EVA exhibiting the lowest crystallization accumulation (7.13 g/m). Molecular dynamics simulations further elucidated the influence of material properties on the diffusion coefficient and binding energy of calcium carbonate crystals, with EVA showing the lowest binding energy with calcium carbonate at 135.11 kcal/mol, ultimately confirming EVA as the optimal material for crystallization prevention. These results offer new strategies and valuable references for managing crystallization in tunnel drainage systems.