The impact factor of airport passenger throughput usually has a lag period. After selecting the influencing factors, the paper determines the lag period of each factor by the random forest importance index. Then, a stepwise regression model for throughput prediction is established using the data of Nanjing Lukou International Airport from 1987 to 2018. Finally, the model effect is evaluated and the throughput of Nanjing Lukou International Airport in 2019 and 2020 is predicted based on the established model. The results show that the influence of impact factors on passenger throughput has a lag period ranging from 1 to 9 years. By comparing with the model without considering the lag period, it is found that the model fitting effect considering the lag period is better and the reduction is significant. Therefore, it is necessary to introduce the lag period into the airport passenger throughput forecast.