A transformation methode of the chromaticity coordinates was proposed to calibrate the measured data obtained by a urine analysis system which implemented in our previous study. Generally. the reacted color of a reagent strip by urine analysis system often exhibit the color distortions due to nonlinear characteristics of the various devices that is the optic module mechanism. hardware, and surround circumstance. A color correction method for minimizing the color distortion play a few role in maintaining high accuracy and reproduction of the urine analysis system. In this work, we used the compensation method such as the shading correction, the characteristic curve extraction of RGB color by means of third order spline interpolation, and linear transformation using a reference color. In addition, 1931 CIE XYZ color space was used to compensate the color of the measured data by a standard reference system as colorimeter. A compensation matrix was obtained so that the output values of the urine analysis system is nearly equal to that of a standard reference system for identical color sample. Color correction obtained by a urine analysis system which implemented in our previous study exhibited a good color accuracy when it was compared with the reference data. Observed result from an experiments on ten items or a urinalysis strip that color difference or between two urine analysis system was 1.28.