<p>This paper proposes a cross-layer scheduling algorithm for joint flow control and resource allocation to optimize the time-average utility function for the dual-connectivity multi-queue multi-server (D-C MQMS) system with a stochastic arrival process. First, we derive the capacity region of the D-C MQMS system by a finite set of linear inequalities. The capacity region characterizes the maximum input rate supported by the system, which is useful for network management. Furthermore, the characterization of the distance between the input rate vector and the boundary of capacity region is exhibited when the channel model is an ON/OFF channel. Then we consider two cases: (I) input rates within the capacity region, and (II) input rates exceeding the capacity region. Two scheduling algorithms for joint flow control and resource allocation, FCRA-I and FCRA-II, are proposed by Lyapunov optimization method. Next, the performance on the utility function and queue delay is analyzed. Finally, by comparing the proposed method with the single-connectivity (S-C) system, we verify the algorithm’s effectiveness by evaluating the average system throughput, system user perceived throughput (SUPT), the throughput-fairness utility function, and the average system backlog.</p>