Heart rate variability is a convenient tool to study the autonomic nervous system of human body. It is a focus of studying cardiovascular disease in clinic. The main spectral components are distinguished in the heart rate variability spectrum: ultra low frequency(ULF),very low frequency(VLF), low frequency(LF), high frequency(HF) components .While different part has different physiological meaning. This paper discusses the design of an effective digital filter for heart rate variability power spectral analysis,which provides a scientific measure of heart rate variability power spectral analysis in further studies and clinical applications.