A white light interferometry micro measurement algorithm based on principal component analysis is proposed to solve the problem of the phase solution in white light interferometry and realize the height measurement of micro morphology. The white light microscopic interference system is used to collect multiple interferograms and reconstruct them into vector form. From a set of interferograms, the background illumination can be estimated by a temporal average, eliminating background light components. Then, the eigenvalues and eigenvectors representing the original data are obtained by a matrix operation. Finally, the phase distribution is calculated by the arctangent function. Experimental results indicate that the measurement result of a standard step height of 956.05 nm by the proposed method is about 953.66 nm and the solution is approximately consistent with the iterative algorithm. In comparison to the iterative algorithm, the processing speed of the proposed method is 2 orders of magnitude faster. The interference fringes with surface roughness of 0.025 μm is analyzed, the mean of the surface roughness calculated by the proposed method is 24.83 nm, and the sample’s standard deviation is 0.3831 nm. The proposed method improves the deficiency of monochromatic interferometry and has the advantages of high speed, low computational requirements and high accuracy.