This paper proposes a novel WOA-based robust control scheme with two kinds of propagation latencies and external disturbance implemented in Software-Defined Wireless Networks (SDWNs) to maximize overall throughput and enhance the stability of the global network. Firstly, an adjustment model developed using the Additive-Increase Multiplicative-Decrease (AIMD) adjustment scheme with propagation latency in device-to-device paths and a closed-loop congestion control model with propagation latency in device–controller pairs are proposed, and the effect of channel competition from neighboring forwarding devices is analyzed. Subsequently, a robust congestion control model with two kinds of propagation latencies and external disturbance is established. Then, a new WOA-based scheduling strategy that considers each individual whale as a specific scheduling plan to allocate appropriate sending rates at the source side is presented to maximize the global network throughput. Afterward, the sufficient conditions are derived using Lyapunov–Krasovskii functionals and formulated using Linear Matrix Inequalities (LMIs). Finally, a numerical simulation is conducted to verify the effectiveness of this proposed scheme.