In order to improve the shafting motion accuracy of two-dimensional turntables such as photoelectric theodolites, we establish a mathematical model considering both the structural error of parts and the coupling amplification effect based on Jacobian-Torsor theory. Aiming at a shafting structure with one fixed end and one swimming, an analysis method of partial parallel structure was proposed. Through numerical simulation analysis, the impact of each part’s structural errors on the motion accuracy of the shafting and the optimal shafting assembly scheme were obtained. The results of assembly and adjustment of a photoelectric theodolite with an optical diameter of 650 mm show that assembly optimization improved the motion accuracy of the shaft system by 32.1%. The precision model and optimization method of shafting motion provide a theoretical basis for the shafting adjustment and tolerance design of two-dimensional turntables such as photoelectric theodolites.