Frequent severe floods have caused great losses to urban safety and the economy, which raises high requirements for the efficiency and effectiveness of emergency rescue. Due to the flood characteristics, flood rescue requires a more rapid responder and decision-making compared with other kinds of disaster rescue. In recent years, aviation emergency rescue (AER) has attracted much attention for flood applications. In order to evaluate the effectiveness of AER for flood disasters, the present study proposes a conceptual model of helicopter AER scheduling and develops a simulation system of helicopter AER scheduling using multiple agents. Seven elements are considered in the conceptual model: helicopters, the command-and-control center, temporary take-off/landing points, mission demand points, resettlement points, loading points, and unloading points. Furthermore, process-oriented and object-oriented scheduling rules are developed as the general guide for scheduling. In order to efficiently simulate and evaluate an AER mission (assisting the decision maker), the simulation system is designed with multiple agents and a user interface, which can quickly load mission settings, run the simulation, and collect data for further evaluation. A standardized mission makespan is adopted as the evaluation index. Based on that, the minimum integrated index can be derived to finally assess the different rescue schemes and choose the best. In the case study, the comparison results indicate that the rescue efficiency of large helicopters (Mi-26 in the case) could be limited by the capabilities of loading points and unloading points. This problem is solved by scheduling small/medium-size helicopters to transfer the personnel. Alternately, two types of helicopters can be used: one for passenger transfer and the other for goods/material transfer. Anyway, the analyses in the case study illustrate the correlation between effectiveness and scheduling, which demonstrates the significance of decision-making. By using the proposed scheduling and modeling methods, the simulation system can be served as a convenient decision-making support tool for practical rescue applications.