The mountainous tectonic zone exhibits high formation heterogeneity, which significantly affects groundwater seepage around the excavated tunnel. Traditional modeling methods that assume the surrounding rock to be a homogeneous field face challenges in accurately predicting and evaluating water discharge within the tunnel. To gain a better understanding of how heterogeneity influences tunnel water discharge, synthetic heterogeneous fields are conducted based on the conceptualization and parameters of the Daxuecheng Tunnel in Chongqing, southwest China. In the heterogeneous modeling, we consider four standard deviations of hydraulic conductivity distribution (0.21, 0.37, 0.55, 0.72) and four dip angles (0°, 30°, 60°, 90°). The results reveal that formation heterogeneity leads to localized instances of significant water inrush and irregular head drawdown distribution, which closely resemble the actual situation compared to the homogeneous model. Generally, the total water discharge into the tunnels increased with increasing heterogeneity and dip angles. Furthermore, the head drawdown in the tunnel region decreased with heterogeneity and increased with dip angles. These findings emphasize the importance of considering formation heterogeneity in tunnel zones and offer valuable guidance for evaluating engineering and environmental challenges in tunnel construction.