Low-altitude aircraft is being developed as a new mode of urban transport. This will give rise to new urban air transport systems, called low-altitude air city transport (LAAT) systems. Recent works show that the Macroscopic Fundamental Diagram (MFD) is a powerful tool for understanding LAAT systems from a theoretical perspective, and allows to detect congestion conditions in the airspace. In this paper, aircraft departures management for LAAT systems with the help of MFD modeling is developed and evaluated. A unique framework, which couples both microscopic and macroscopic levels of LAAT operation, is established. The plant model considers the microscopic level, where an aircraft collision-avoidance model with a cooperative control algorithm from the literature is implemented to describe the low-altitude aircraft interactions, implying the microscopic traffic behavior. At the macroscopic level, an accumulation-based model for distributed regions is introduced, which is used as the control model. Then, based on the developed framework, an optimal control strategy is formulated to optimize the aircraft inflow rate by manipulating their departure times to mitigate congestion. Different control strategies are tested: Greedy Controller and Model Predictive Controller. The strategies are deployed for the whole network or for each region at the macroscopic level and then transformed to the microscopic level. This study demonstrates that the MFD-based traffic control strategies can reduce congestion in LAAT systems.