The integration of Maritime Internet of Things (M-IoT) technology and unmanned aerial/surface vehicles (UAVs/USVs) has been emerging as a promising navigational information technique in intelligent ocean systems. With the unprecedented increase of computation-intensive yet latency sensitive marine mobile Internet services, mobile edge computing (MEC) and non-orthogonal multiple access (NOMA) have been envisioned as promising approaches to providing with the low-latency as well as reliable computing services and ultra-dense connectivity. In this paper, we investigate the energy consumption minimization based energy-efficient MEC via cooperative NOMA for the UAV-assisted M-IoT networks. We consider that USVs offload their computation-workload to the UAV equipped with the edge-computing server subject to the UAV mobility. To improve the energy efficiency of offloading transmission and workload computation, we focus on minimizing the total energy consumption by jointly optimizing the USVs’ offloaded workload, transmit power, computation resource allocation as well as the UAV trajectory subject to the USVs’ latency requirements. Despite the nature of mixed discrete and non-convex programming of the formulated problem, we exploit the vertical decomposition and propose a two-layered algorithm for solving it efficiently. Specifically, the top-layered algorithm is proposed to solve the problem of optimizing the UAV trajectory based on the idea of Deep Reinforcement Learning (DRL), and the underlying algorithm is proposed to optimize the underlying multi-domain resource allocation problem based on the idea of the Lagrangian multiplier method. Numerical results are provided to validate the effectiveness of our proposed algorithms as well as the performance advantage of NOMA-enabled computation offloading in terms of overall energy consumption.