Based on the mathematic representation of loops of kinematic chains, this paper proposes the "" operation of loops and its basic laws and establishes the basic theorem system of the loop algebra of kinematic chains. Then the basis loop set and its determination conditions, and the ways to obtain the crucial perimeter topological graph are presented. Furthermore, the characteristic perimeter topological graph and the characteristic adjacency matrix are also developed. The most important characteristic of this theory is that for a topological graph which is drawn or labeled in any way, both the resulting characteristic perimeter topological graph and the characteristic adjacency matrix obtained through this theory are unique, and each has one-to-one correspondence with its kinematic chain. This characteristic dramatically simplifies the isomorphism identification and establishes a theoretical basis for the numeralization of topological graphs, and paves the way for numeralization and computerization of the structural synthesis and mechanism design further. Finally, this paper also proposes a concise isomorphism identification method of kinematic chains based on the concept of characteristic adjacency matrix.