Based on. generalized topological figures of kinematical chains, all-loop-link-join-matrix is built, which contains all information of kinematical chains. The constructive principle and method of that matrix is put forward. It is applied in the research of the Isomorphism Identification of kinematical chains. The method and the main process of the Isomorphism Identification of kinematical chains is given out further. Some practical examples are solved by the new method. The matrix contains all loops of kinematical chains, and solves forky problems in the choice of loops. It cannot be constrained by the bars and the freedom of kinematical chains. In the matrix, elements are fewer; the amount of calculation is little, and the speed of calculation is high, so the method can be realized in computer. Because of the use in computer, the method is efficient and reliable. The method is certified by tremendous examples, especially in the Isomorphism Identification of kinematical chains which contain many bars and loops.