To monitor the quality of sapphire substrate processing， a specific system for sapphire substrate surface morphology measurement and evaluation was developed. The classic vertical scanning white light interference technology was adopted. Based on the fluctuation of the interference images， the cross-section variance calculation method was used as the definition evaluation method to realize the automatic focusing of the system. Referring to the substrate measurement points and their location distribution recommended by the national standard GB/T 29505-2013， the corresponding measurement points for different sizes of sapphire substrates were increased according to the distance between adjacent centers of the same layer unit circle. Two-dimensional and three-dimensional roughness evaluation parameters were selected as the system evaluation parameters. The multi-point location roughness statistical parameters were analyzed. The error of the system was compensated by standard parts with R_a values of 0.1， 0.2， 0.4， and 0.8 μm， and the error compensation equation was obtained. The commercial 3D optical profilometer Zygo7300 was used to perform comparative experiments， and five different positions of the standard part with 0.8 μm R_a were measured. The error range of R_a measured by the two interferometers is -0.012-0.011 μm. After the error compensation， the 2-inch and 4-inch sapphire substrates were measured and evaluated. The experimental results show that the accuracy of the measurement system has a nanometer level， and it can measure and analyze the surface morphology of sapphire substrates with different sizes as well as evaluate the surface quality distribution.