A method for analyzing the mechanism structure was presented. The multiple joints in the schematic diagram could be offset into the separate joints with imaging zero distances, drew them in small distances between them rather than drew them concentrically. With former representation, the topological graph and its incidence matrix were easily built to represent the topological structures of a kinematic chain or a mechanism with multiple joints. When the basic closed loops were calculated with the tree and co-tree matrix got from the incidence matrix, all of the loops in a kinematic chain or a mechanism could be got based on the linear combination of the basic loops. Combining such joints that actually jointed at a single location into its original single symbol,multiple joint, again and then sorting the loops with the weights of each loop, some optimum loops with independence from each other and with joint connectivity in a loop were selected. The research showed that the topological graphs are simple and directly perceptible, and the algorithms for producing the incidence matrix and analyzing closed loops could be conveniently used for programming software for automatic structural and kinematic analysis of mechanism.