Airport disruptions often pose challenges in assigning aircraft to gates, resulting in infeasible planned schedules. In particular, a large number of transfer passengers miss their connections in the context of disruptions, which cause huge economic losses to airlines and serious passengers’ dissatisfaction. This paper proposes a set-partitioning-based model to optimize Aircraft-Gate Reassignment with Transfer Passenger Connections (AGRP-TPC), which incorporates flexible gate-swap and aircraft-delay operations to mitigate the overall impact of disruptions. To efficiently solve the model, we introduce the concepts of additive-transfer and nonstop-transfer to handle passenger connections, and develop a Hierarchical Column-and-Row Generation (HCRG) approach guided by airport terminal space attribute. The column generation and row generation procedures solve iteratively until no new variables and constraints are generated. In addition, a follow-on strategy and a diving heuristic are designed to efficiently obtain high-quality solutions. We evaluate the proposed approach using various instances from a major Chinese international airport. Computational results demonstrate that our approach outperforms the comparison algorithms and produces good solutions within the time limit. Detailed results indicate that our approach effectively reduces overall losses in aircraft-gate reassignment following disruptions, and it can serve as an auxiliary decision-making tool for airport operators and airlines.