The civil aviation transport due to the closed environment inevitable is an important route for the global spread of respiratory diseases. In order to reduce the probability of infection of passengers, an improved wells-reily model for cabin passenger risk assessment have been given in this work, the cabin ventilation and passenger nose and mouth orientation were considered and the effectiveness of the model was verified with published data. And the association between load factor, empty seat use scheme and the number of infected people were finally discussed. The results show the number of infected people is positively correlated with the passenger load factor, and the most suitable load factor can be determined by controlling the final number of infected people with the condition of the epidemic situation in the departure city. The results also show passengers in the window position are less likely to be infected than in the aisle position, and the empty seats are arranged in the aisle can reduce the probability of infection by up to 9.11%. By using the model, the airlines can seek the full load factor threshold and seat use scheme to improve economic benefits and reduce the probability of infection of passengers.