In precision machining, the surface geometry of a device is one of the important parameters that directly affects the device performance. This paper proposes nonequal arm surface measurement of femtosecond optical frequency combs (OFCs) using the Savitzky-Golay filtering algorithm, which uses the high spatial coherence of OFCs to realize high-precision, nonequal surface measurements. The Savitzky-Golay filtering algorithm and a high-order polynomial envelope fitting algorithm are used to smooth and denoise the interference signals to improve signal quality and measurement accuracy. The experiments are carried out under the condition of nonequal arms, and the results show that the repeatability is 28.6 nm for 20 consecutive measurements on the step surface of a 0.5 mm gauge block. The frosted glass surface is measured 20 times, and the measurement repeatability at the center position is 89.6 nm, which verified the system capability of nonequal arm high-precision measurement under different reflective surfaces.