Three-dimensional (3D) profile measurement is an indispensable process for assisting the manufacture of various optic, especially aspheric surfaces. This work presents the measurement error calibration of a 3D profile measurement system, namely PMI700. Measurement errors induced by measuring tool radius, alignment error and the temperature variation were analyzed through geometry analysis and simulation. A quantitative method for the compensation of tool radius and an alignment error compensation model based on the least square method were proposed to reduce the measurement error. To verify the feasibility of PMI700, a plane and a non-uniform hyperboloidal mirror were measured by PMI700 and interferometer, respectively. The data provided by two systems were high coincident. The direct subtractions of results from two systems indicate RMS deviations for both segments were less than 0.2l.