In order to test 3D profile of micro/nano structures with high resolution, a measurement system was developed based on microscopic interferometry and polarization technique. First, five interferograms with π/2-phase increase were acquired by five-step phase-shift interferometry. Then wrapped phase maps were calculated with Hariharan five-step-phase-shift algorithm. Finally, 3D profile of micro/nano structure could be gotten with branch-cut unwrapping algorithm and the phase-height formula. A polarizer provided a polarization beam and adjusted its illumination power. The polarized beam was parceled into two perpendicular directions by a polarization-beam splitter, and the intensities proportion of the two beams could be adjusted by rotating a 1/2-waveplate making it possible to compensate the differences of the reflectances between the sample and the reference mirror. This arrangement allowed that the interferograms had the advantages of high contrast and optimum intensity, and this was useful to increase system resolution. The system’s main performance parameters include the Ra-repeatability-measurement resolution better than 0.06 nm, the error indication better than ±1%, and the variation of indication better than 0.5%. The experimental work conducted on several typical micro/nano structures such as standard multi-indents structures, Si-microphone membranes and Si-micro-gyroscope folded-beams confirms that such a measurement system is efficient to characterize 3D profile of micro/nano structures with high resolution.