A high precision step height measurement system, which is based on wavenumber resolved low coherence interferometry, is presented. The information of the measurand is obtained with a fiber Michelson interferometer which is sourced by a broadband light source. The broadband spectrum interferometric beam is dispersed with a bulk dispersing grating to be an optical plate in which the wavelengths are continuously distributed. The optical plate is detected with a linear array charge coupled device (CCD). By transforming the wavelength spectrum of the interferometric signal into wavenumber spectrum, absolute optical path difference of the interferometer can be measured precisely by measuring the wavenumber difference between two neighboring peaks of the wavenumber spectrum. By shorting the length of the interferometric arms in the optical fiber Michelson interferometer, the environmental disturbances are depressed and high measurement precision is obtained. The measurement resolution is as high as 6.03 nm. A step height with the calibrated value of 50 μm that is configurated with two gauge blocks is measured by the system. The standard deviation of 10 times measurement results is 6.8 nm.