To solve the instability problem of established sample in the neural network evaluation method for mine ventilation system, a comprehensive evaluation of the ventilation system is carried out based on rough sets and BP neural networks. Taking the ventilation system of a mine as an example, the classification quality of raw data samples are tested by using rough set data analysis system. Then, based on artificial neural network theory, a rough sets-neural network evaluation model of a mine ventilation system is established and a new rough sets-neural network evaluation method of mine ventilation system is formed. The results show that, after the model validation of data and application, its theoretical evaluation results are in line with the actual situation, and the network total error is less than 0.004. It shows that the comprehensive evaluation method based on rough sets-neural networks has a good effect in evaluating mine ventilation system in practical application.