Crystallization-induced blockage in tunnel drainage pipes poses a serious threat to the long-term safe operation of tunnels. Carbon dioxide (CO?) is a critical environmental factor influencing the crystallization process, yet the mechanism by which its concentration governs this process remains poorly understood. To address this, an indoor simulation experiment was conducted to model the crystallization that occurs in the drainage system after groundwater flows through the concrete initial support. Four CO? concentrations—0.04%, 1%, 2%, and 5%—were tested under a constant temperature of 20?°C and cyclic flushing conditions over a 30-day period. Changes in pH and the mass of crystals formed were monitored, and the precipitates were characterized using scanning electron microscopy (SEM) and X-ray diffraction (XRD).The results showed that the total crystal mass increased significantly with rising CO? concentration (the maximum mass over 30 days was up to 3.65 times that at the lowest concentration), but the growth rate gradually declined. The incremental crystal mass per unit CO? concentration dropped sharply from 2.91–3.48?g/%CO? in the low-concentration range to 1.20?g/%CO?, representing a 65.5% decrease. The pH evolution exhibited a three-stage pattern of a rapid increase followed by a slow decrease and eventual stabilization; higher CO? concentrations resulted in lower peak and stable pH values. Crystal type and morphology were markedly regulated by the CO? concentration. At low concentrations, well-crystallized calcite was predominant; at 2% CO?, a small amount of vaterite appeared and formed intergrowth structures; at 5% CO?, vaterite became the dominant crystalline phase. Furthermore, kinetic analysis indicated that increasing the CO? concentration significantly accelerated the CaCO? crystallization rate, but the rate constant displayed a non-monotonic change. This behavior is attributed to the competition among different crystal phases and adjustments in the crystallization pathway during phase transformation. This study provides valuable insights for the prevention and control of drainage system blockages.