Entering airline cargo alliance has become one of the major strategies for air cargo carriers in a competitive environment. The majority of studies on airline alliances were focused on the air passenger alliances. Few studies have examined air cargo alliance practices; nonetheless, no research has been paid to the decision-making problem on selecting allied routes with alliance types and the allied flight network issues for the airline cargo alliances. This study develops a series of models to analyze the airline cargo alliance decision-making and determine allied flight frequencies under air cargo alliances. A fuzzy cooperative game for assessing the combination of airline cargo alliance alternatives was developed. Under the determined airline cargo alliance condition, the integrated allied cargo flight network programming model was developed, while mutually considering overall profitability, traffic gains, and cost reduction for the allied network in which they cooperate with their partners. A numerical case study demonstrated the synergy benefits of airline cargo alliances and the feasibility of applying the proposed models. The results of this study explored the effects of airline cargo alliances on allied routes and flight frequencies, and the allied network structure. In addition, it is envisaged that the results of this study may shed light on airline cargo alliance strategies.