This paper proposes a five degrees-of-freedom measurement system for measuring geometric errors of the rotary axis. To align the measured rotary axis with the reference axis, a diode laser is used to represent the rotary axis of the measured rotation stage. Based on the proposed measurement system, a model for separating the position independent geometric errors and position dependent geometric errors of the measured rotary axis from the measured value is established and verified by measurement experiments. The results of measurement experiments repeated for five times show that the measurement uncertainty of the proposed measurement system is less than ±1.6 µm for radial motion, the measurement uncertainty is less than ±1.7 arc sec for tilt motion, and the measurement uncertainty is less than ±1.3 arc sec for angle position.