The digital twin model of mine ventilation system (DTMVS) plays an important role in intelligent safety management. However, the uncertainty of the ventilation resistance coefficient, which is the core parameter of the model, makes it challenging to accurately construct a DTMVS. In this study, Latin Hypercube Sampling (LHS) and ventilation resistance coefficient estimation models (VRCEMs) are used to analyze the uncertainty. First, the LHS method was used to explore the effect of uncertainty in the simulated airflow by continuously increasing the level of uncertainty in the ventilation resistance coefficients. Subsequently, the ventilation resistance coefficients were estimated using the VRCEMs, and the uncertainty of the ventilation resistance coefficient and the simulated airflow was analyzed. The results showed that the ventilation resistance coefficients with a 5% coefficient of variation can cause the DTMVS to lose 34% of the real airflow data points. The degree of uncertainty in the ventilation resistance coefficients estimated by the VRCEM-GA (VRCEM using genetic algorithm) and VRCEM-DE (VRCEM using differential evolution algorithm) methods was enhanced by 27.4% and 4.4%, respectively, compared with VRCEM-ES (VRCEM using evolutionary strategy algorithm). The VRCEM-ES model had the least influence on the uncertainty of the simulated airflow of DTMVS. The simulated airflow of the DTMVS constructed based on VRCEMs fluctuated normally within the confidence interval. VRCEMs had a higher sensitivity to the ventilation resistance coefficients of branches with low coefficients of variation.