Optical transport network (OTN) is widely used in backbone and metro area transmission networks to increase network transmission capacity. In the OTN, it is particularly crucial to rationally allocate routes and maximize network capacities. By employing deep reinforcement learning (DRL) and software-defined networking (SDN) based solutions, the capacity of optical networks can be effectively increased. However, because most DRL-based routing optimization methods have low sample usage and difficulty in coping with sudden network connectivity changes, converging in software-defined OTN scenarios is challenging. Additionally, the generalization ability of these methods is weak. This paper proposes an Ensembles and Message passing neural network-based Deep Q-Network (EMDQN) method for optical network routing optimization to address this problem. To effectively explore the environment and improve agent performance, the multiple EMDQN agents select actions based on the highest upper-confidence bounds. Furthermore, the EMDQN agent captures the network’s spatial feature information using a message passing neural network (MPNN) based DRL policy network, which enables the DRL agent to have generalization capability. The experimental results show that the EMDQN algorithm proposed in this paper performs better in terms of convergence. EMDQN effectively improves the throughput rate and link utilization of optical networks and has better generalization capabilities.