Because of the limitation of sampling equipments and sampled signal, it is hard to sample uniformly, and nonuniform sampling is widely used actually. When data are not sampled uniformly, the sampling theorem no longer applies. It’s effective to analysis the spectrum of the nonuniformly sampled signals by the means of spectrum analysis based on least square technique. The reason for spectral noise and its influence factors are discussed detailedly. Because some weak signal are inundated with the spectral noise, the method of amplitude damping based on least square technique is used to suppress the strong signal and spectral noise effectively. The weak signal, of which the amplitude is one hundred million times smaller than the strong one, is detected successfully in the simulation experiment, and the parameters of the components of nonuniformly sampled signal can be estimated with high accuracy.