As the geometric errors of shafts in a femtosecond laser tracker directly lead to pointing error and limits the coordinate measuring accuracy of the instrument, this paper researches the effects of geometric errors between optical axis and vertical rotary shaft in the laser tracker on measuring accuracy of the instrument. It proposes a calibration method for the coaxiality of optical axis and vertical rotary shaft to reduce the tracking measuring errors from the misalignment between optical axis and vertical rotary shaft. Firstly, a mathematical model of geometric errors between optical axis and vertical rotary shaft was built based on geometrical optical principles, and influences of the tilt and translation between optical axis and vertical rotary shaft on measuring angle errors were analyzed. Then, a coaxiality detecting method based on the rotation imaging principle and image processing algorithm was proposed, and a set of coaxiality detecting device was designed. On the basis of the detecting device, the tilt and translation between optical axis and vertical rotary shaft were calibrated by adjustment of dual wedges. Results show that the angle error of optical axis and vertical rotary shaft is 3.4″ and the translation error is 26.1 μm after calibration, which meets the design indicator of femtosecond laser tracker. This work establishes a theoretical foundation for the subsequent system errors.