When mines have entered into the deep resource exploitation, the ventilation resistance will increase, and thus it is necessary to reduce the resistance of mine ventilation. This paper comprehensively selected the indexes of technology, economy, safety and stability to establish the comprehensive evaluation model AHP-FPR of mine ventilation system reduction and optimization. It has also carried out the ventilation parameter network calculation and comprehensive evaluation of four reduction and optimization schemes, such as ventilation system’s network structure adjusting, shortening public tunnel length, enlarging basal area, and changing main diagonal branch wind resistance. Finally, the optimum scheme is defined.