A measurement method for the lens centering error based on double phase-encoding optical Joint Transform Correlator(JTC) was proposed for improving the measuring accuracy and determining the orientation of the centering error. On the basis of the principle of traditional JTC, two phase functions were utilized to code the reference image and the joint power spectrum, and proper filters were chosen to eliminate the effect of the sidelobe and to obtain an output with one cross-correlation peak. Then, this JTC technique after double phase-encoding was used to detect the displacement vectors between target images and reference image and to fit a circle using the displacement vectors. The vector between the center of the fitting circle and a certain point on the fitting circle is the magnified centering vector of corresponding angle, which means that the size and orientation of the centering error have been determined simultaneously. The experimental results show that the outputs keep only one speculate cross-correlation peak after double phase-encoding, which implements the displacement measurement with sub-pixel accuracy. This technology is used to measure the centering error of a lens accurately, the experimental standard deviation is 0.1 μm, and the biggest absolute error is 0.3 μm, which meets the requirement of centering error measurement.