The aim of this paper is to propose a practical solution for mechanism kinematic chain isomorphism identification – an artificial fish swarm algorithm. The artificial fish model of mechanism isomorphism identification is established, and behavioral way of the artificial fish is designed. According to isomorphism identification features of topological graph, the process of mechanism isomorphism identification based on artificial fish swarm algorithm is confirmed. The rationality and reliability of artificial fish swarm algorithm on the isomorphic identification of mechanism have been illustrated by a specific example, which provides a new method for intelligent CAD system design of mechanism. It builds a basis for future work in isomorphism identification of mechanism with high efficiency. Isomorphic identification of mechanism will contribute to rational qualitative analysis of mechanism design, perfection of irrationality can be done timely, which is the key factor for mechanical manufacturing. In this paper, we introduce the mechanism kinematic chain firstly, then optimization of artificial fish swarm algorithm is illustrated, and it is shown that how fish swarm algorithm is applied to mechanism kinematic chain. Finally, the feasibility and efficiency of the method are verified by the example of 10 bars, and the complex mechanism can be identified by the example of 14 bars and 18 bars.