This paper investigates the effects of new airport on a multi-airport system (MAS) with air-rail integration service and heterogeneous passengers. Vertical structure models are proposed to capture the interactions among the stakeholders: passengers, airlines, and rail operator. In the proposed models, passenger heterogeneity is reflected by a continuous value-of-time (VOT) distribution, and the total passenger demand is given. The critical VOTs dividing the passengers into different groups by travel mode are identified, and the distributional effects of new airport and air-rail cooperation on the heterogeneous passengers are examined. The findings show that the new airport and air-rail cooperation can benefit all passengers, and these benefits vary significantly across passengers. The poorest passengers gain the most from the air-rail cooperation. However, who gains the most from the new airport depends on the transfer time and cost for the new airport service. For a relatively low transfer time and cost, the mid-income passengers gain the most. Otherwise, the low-income passengers gain the most. At a high congestion level of the hub airport, introducing a new airport is more efficient in decreasing the social cost of the system than introducing the air-rail cooperation. Conversely, at a low congestion level of the hub airport, introducing a new airport may cause an increase in the social cost of the system instead. Consequently, the decision of investing in a new airport in an MAS should be carefully made.