Using earth air tunnel heat exchangers (EATHE) to pre-treat air entering underground space is an effective measure for energy-saving. This paper addresses the scarcity of numerical model for heat and mass transfer in long, separated air intake tunnels by establishing a three-dimensional model that considering condensation, specifically analyzing the heat transfer process in tunnels with separated ventilation earth air tunnel heat exchanger (SV-EATHE). The accuracy of the model was verified by engineering measured data. The heat transfer performance of EATHE and SV-EATHE is compared and analyzed by using the model. The results indicate that the annual heat exchange of SV-EATHE is approximately 80 % of that of EATHE, with the latent heat exchange from March to September accounting for 77.2 % of EATHE's. SV-EATHE significantly reduces condensation in traffic tunnels. Increasing ventilation will correspondingly increase the heat exchange and reduce dehumidification, but the rate of change will gradually decrease. The change in partition wall thickness has an approximately linear relationship with the amount of heat exchange. For every 0.1 m increase in diaphragm wall thickness, the heat exchange in the intake duct in August is reduced by approximately 1500 kWh and the dehumidification is reduced by approximately 0.6 kg/h.