Because of the advantages such as the large measurement range, high accuracy and not needing cooperation target, frequency modulation continuous wave (FMCW) laser radar plays an important role in metrology and industrial measurement. This paper briefly introduces the basic structure and ranging principle of frequency modulation continuous wave laser radar, which was based on equal frequency sampling method. The main noises that exist in the auxiliary interference signal and the measurement interference signal and their characteristics were analyzed. When the auxiliary interference signal of the system was existed with noise, part of the extreme points was incorrect and the measurement error will be brought into the result. Subsequently, the Cramer-Rao lower bound was adopted to evaluate the influence of the noise that existed in the measurement interference signal. To improve the accuracy and stability of the measurement, the adaptive filtering methods of wavelet threshold filter based on EMD and Hanning band-pass filter based on wavelet filtering were used to reduce the noise existing in auxiliary interference signal and the measuring interference signal, respectively. In the experiments, a flat mirror and a variety of roughness blocks were measured very times and the correctness was verified by comparing the measured results of the system with a precision guide. Experimental results showed that：when the measured object was located at stand-off distance of about 3.9 m, the adaptive filtering methods can effectively remove the noise and the measurement uncertainty of the mirror and the roughness blocks was 20 μm and tens of microns respectively (K=2), which was much smaller than the uncertainty of the wavelet filtering method (120 μm and hundred microns). At the same time, by comparing the displacement value of the precise guide rail and the measurement results of the system, it proves that the proposed method in this paper can effectively improve the measurement accuracy of the system.