A precise 3D surface measurement method for large stepped structures without height ambiguity is proposed based on optical-frequency-comb-referenced frequency-sweeping interferometry and Fourier-transformed fractional phase retrieval. Unlike other interferometry that depends on the absolute phase value for several certain wavelengths, this method obtains results from the phase change during frequency sweeping and thus remains free from the confined non-ambiguity range. By reference to an optical frequency comb, the relative uncertainty from the tunable laser frequency was reduced by three orders of magnitude, and the sweeping frequency range can be precisely determined. Besides, the fractional phase can be rapidly retrieved in only one step using a Fourier transform method, with advantages of high accuracy and immunity to light intensity fluctuation and mechanical vibration noise. Samples of step heights from 1 μm to 1 mm were measured, and the standard uncertainty was 45 nm. This permits applications such as quality assurance in microelectronics production and micro-electro-mechanical system (MEMS) manufacture.