Self-collision detection is fundamental to the safe operation of multi-manipulator systems, especially when cooperating in highly dynamic working environments. Existing methods still face the problem that detection efficiency and accuracy cannot be achieved at the same time. In this paper, we introduce artificial intelligence technology into the control system. Based on the Gilbert-Johnson-Keerthi (GJK) algorithm, we generated a dataset and trained a deep neural network (DLNet) to improve the detection efficiency. By combining DLNet and the GJK algorithm, we propose a two-level self-collision detection algorithm (DLGJK algorithm) to solve real-time self-collision detection problems in a dual-manipulator system with fast-continuous and high-precision properties. First, the proposed algorithm uses DLNet to determine whether the current working state of the system has a risk of self-collision; since most of the working states in a system workspace do not have a self-collision risk, DLNet can effectively reduce the number of unnecessary detections and improve the detection efficiency. Then, for the working states with a risk of self-collision, we modeled precise colliders and applied the GJK algorithm for fine self-collision detection, which achieved detection accuracy. The experimental results showed that compared to that with the global use of the GJK algorithm for self-collision detection, the DLGJK algorithm can reduce the time expectation of a single detection in a system workspace by 97.7%. In the path planning of the manipulators, it could effectively reduce the number of unnecessary detections, improve the detection efficiency, and reduce system overhead. The proposed algorithm also has good scalability for a multi-manipulator system that can be split into dual-manipulator systems.