To realize the ultra-precision measurement for tip arc waviness of diamond tools, an arc profile measurement system based on an atomic force microscopy and an ultra-precision spindle was established. The evaluation method of tool tip arc waviness and the scheme to control measuring error were investigated. Firstly, the selection principle of waviness cut-off wavelength was proposed in the arc waviness evaluation and the flowchart of tool tip arc waviness measurement was presented. Then, the measurement and evaluation for radial rotation errors of the ultra-precision spindle were discussed, the control for mounting errors of eccentric and declination angles and the calibration for nonlinear error of atomic force scan system were described. Finally, the tip arc waviness of a diamond tool was measured by self-developed ultra-precision profile measurement system, and the measurement accuracy and uncertainty were analyzed. Experimental results show that the tip arc waviness of diamond tools can be accurately described by proposed method, the waviness is 0.106 μm,and the uncertainty is 23.8 nm. These results satisfy the system requirements for higher precision and stabilization.