Slot allocation in a single airport aims to maximize the utilization of airport-declared capacity under operational and regulation constraints, while that in a multi-airport system (MAS) has to take airspace capacity into account. This is due to the fact that the conflict of using the limited capacity of certain departure/arrival fixes in the terminal airspace could induce unnecessary flight delays. The uncertainty of flying times between the airport and congested fixes makes it even more complicated for slot allocation in a MAS. Traffic flow may exceed capacity when the flying times of flights change. In this paper, the authors propose an uncertainty slot allocation model for a MAS (USAM). The objective of the model is to minimize the total displacement of slot requests in the MAS while considering all of the capacity constraints, as well as the uncertainty of flying time. The constraints of departure/arrival fixes are formulated as chance constraints, and then the Lyapunov theorem is applied for reformulation. The USAM is applied in the MAS of the Guangdong-Hong Kong-Macao Greater Bay Area (GBA). Specifically, the impact of the uncertainty of flying times from five airports to airspace fix YIN is investigated. Results show that the total displacement would increase if the uncertainty of flying time was considered. The optimized schedule using the USAM, however, is more robust and can satisfy capacity constraints under various scenarios.