To accurately measure the thickness of the radial GRIN lens， the measurement error caused by eccentricity was studied. First， the working principle of the spectral confocal thickness measurement system was introduced. Then， the thickness measurement model for the radial GRIN lens was established by using the ray trace equation， optical Lagrange function， and ray arc differential equation in the Cartesian coordinate system. The thickness measurement error caused by the eccentricity of the radial GRIN lens was analyzed through theoretical research and simulation， and the experimental platform was built. The thickness measurement was completed by using the precision displacement table to drive the GRIN lens to simulate lens eccentricity. The experimental results show that the thickness measurement error of radial GRIN lens increases with the eccentricity. The influence of axial measurement position on the thickness measurement is negligible. The accuracy of the theoretical analysis is verified. The thickness measurement error of the GRIN lens with an actual thickness of 4.012 6 mm is 4.6 μm after correcting for eccentricity. This indicates that the spectral confocal method can realize the precise measurement of radial GRIN lens thickness.