Isomorphism identification plays an important role in structural design and innovative design. Based on the adjacency matrix and loop theory, a new method is proposed in this paper to identify the isomorphic kinematic chains. It enriches the application of loop-based theory for isomorphism identification. In the kinematic chain, links and joints are connected alternatively and every link corresponds to a fixed link degree. Due to the inherent characteristics, the labeled sequence of links can be random, which does not affect the result of isomorphism identification. By the programming software MATLAB, some examples with 6-, 8-, 10-, 11-, 12-link kinematic chains, and 15-vertex topological graphs are presented. Results show that the proposed method applies to topology graphs and kinematic chains with one or multiple joints. Compared with other methods, the proposed method is confirmed correctly. And there is no counterexample. It lays a solid foundation for structural synthesis in the future.