In this paper, based on perimeter topological graphs of kinematic chains, many novel topological concepts including the synthetic degree-sequence, the characteristic adjacency matrix and the characteristic representation code of kinematic chain are proposed. Both the characteristic adjacency matrix and the characteristic representation code are unique for any kinematic chain and easy to be set up. Therefore a quite effective isomorphism identification method is presented depending on the characteristic adjacency matrix. It high effectiveness is proved by many examples. With object-oriented programming language, a program which can sketch topological graphs of kinematic chains has been developed based on the characteristic representation code. Finally, an application software system establishing the atlas database of topological graphs is introduced. And some functions about the atlas database are also presented in this paper.Copyright © 2005 by ASME