As an important part of the fifth generation (5G) mobile networks, unmanned aerial vehicles (UAVs) have been applied in various communication scenarios due to their high operability and low cost. In this paper, we investigate a multi-UAV communication system with moving users and consider the co-channel interference caused by the transmissions of all other UAVs. To ensure the fairness, we maximize the minimum average user rate during the observed time by jointly optimizing UAVs’ trajectories, transmission power, and user association. Considering that UAVs can cover a large area for communications, UAVs do not need to move as soon as the users move. Therefore, a two-timescale structure is proposed for the considered scenario, where the UAVs’ trajectories are optimized based on the channel state information (CSI) in a long timescale, while the transmission power and the user association are optimized based on the instantaneous CSI in a short timescale. To effectively tackle this challenging non-convex problem with both discrete and continuous variables, we propose a joint neural network (NN) design, where a deep reinforcement learning based Pointer Network named advantage pointer-critic (APC) is applied to optimize discrete variables and a deep-unfolding NN is used to optimize the continuous variables. Specifically, we first formulate a Markov decision process to model the user association, and then employ the APC network trained by the advantage actor-critic algorithm to address it. The APC network consists of a Pointer Network and a Multilayer Perceptron. As for the deep-unfolding NN, we first develop a block coordinate descent based algorithm to optimize the UAVs’ trajectories and transmission power, and then unfold the algorithm into a layer-wise NN with introduced trainable parameters. These two networks are jointly trained in an unsupervised fashion. Simulation results validate that the proposed joint NN significantly outperforms the optimization algorithm with much lower complexity, and achieves good performances on scalability and generalization ability.