Kinematic and dynamic performances of a robot mechanism is, to some extent, determined by its topological structure, so topological structure analysis and synthesis is an important tool to research and application of robot mechanisms. However, there is still no software for automatic structure analysis of robot mechanisms. The efficiency of manual analysis method is too low and it is difficult to get a complete result. In order to solve this problem, a digital modeling method for topological structure of robot mechanisms was proposed, and the automatic generation algorithm for position and orientation characteristic set (POC) of robot mechanisms was presented. The digital modeling for robot mechanisms was showed, including mathematical description of topological structure elements and the corresponding data structure. Secondly, the essence of POC set was uncovered, and the operation rules of POC for serial and parallel robot mechanisms were formulated based on the theory of linear dependence. Furthermore, the automatic generation algorithms of POC for serial and parallel robot mechanisms were achieved. Finally, five examples were provided to verify the efficiency of the digital modeling method and automatic generation algorithm mentioned above. The digital modeling method for topological structure and automatic generation algorithm of POC presented would be parts of the software being developed for automatic structure analysis and synthesis of robot mechanisms.