The routing algorithm based on a single routing metric parameter is difficult to meet the Quality of Services (QoS) requirements of multi-source data flows in the software-defined factory heterogeneous network, resulting in link congestion and waste of network resources. To solve the problem, this paper proposes a QoS optimization method for software-defined factory heterogeneous networks based on the double deep Q network (DDQN). First, a QoS optimization architecture is proposed for software-defined factory heterogeneous networks, and the optimization function for network latency and load balancing is established. Then, the DDQN algorithm is used to obtain the optimal paths of multi-source data flows, and the optimal path is uniformly issued by the software-defined network controller. Experiments showed that the proposed algorithm has good convergence and generalizability. Compared with the existing algorithms, it outperforms in network latency, network jitter, and network throughput, improving network load balancing and routing efficiency. This research is able to provide a solution to the QoS optimization and dynamic traffic scheduling in smart heterogeneous networks and provide a technical reference point for realizing customized smart factories.