In order to know the feasibility that the modern spectrum analysis ways are applied in wind profiler, the fast Fourier transform (FFT) and maximum entropy method (MEM) are contrasted by using simulation data and radar measurement data respectively. The result shows：(1）When the radar echo is strong, the effect of two methods are equivalent. But when the echo is weak, the MEM spectra are better than others. The MEM can powerfully remove the ground clutter contaminant. (2）The MEM spectra are smooth, so it can be used to reduce white noise influence also. (3）The iterative steps in MEM have some influence on the spectrum. The step calculated by final prediction error（FPE）rule is less. Using 15 steps in MEM can get a better result. The wind profiler radar echo is weak usually, so the conclusions of this paper can help improve the effect of spectrum analysis.