Objective：To study the effect of respiratory frequency on spectral components of rabbit heart rate variability（HRV） and to discuss how to exclude it. Methods：Totally 12 healthy male rabbits aged 4-5 months and weighting 2.5-3.0 kg were selected. Rabbit respiratory control system was established. Electrocardiograph，instant blood pressure and respiratory waveform under different respira－tory frequencies（RF）（40，50，60 times/min） were recorded synchronously via SKY-A4（a three channel electrophysiolograph）. HRV ＆ BRS2.0-a HRV analysis system was used to observe the shift of high frequency peak（HFP） and to analyze power spectra density（PSD）. Two different analysis methods were adopted to analyze PSD：traditional heart rate variability（tHRV） analysis method and enhanced heart rate variability（eHRV） analysis method. Comparison between the results of the two methods was made. Results：①the shift of HFP：HFP was located at the conjunction of low frequency（LF） segment and high frequency（HF） segment when RF 50 times/min；HFP shifted into the LF segment when RF 40 times/min；total HFP shifted to HF segment when RF 60 times/min. ②tHRV results：RF exerted no effect on total power while significantly affected LF，LFnorm，HF，HFnorm. Compared with those when RF 50 times/min，HF and HFnorm decreased（P=0.179，P=0.011）while LF，LFnorm，LF/HF increased（P=0.04，P=0.001，P=0.028） when RF 60 times/min. Compared with those when RF 50 times/min，HF and HFnorm decreased while LF，LFnorm，LF/HF increased when RF 40 times/min.③eHRV results：there was no significant difference in LF，LFnorm，HF，HFnorm，LF/HF when RF 60 times/min and RF 40 times/min compared with those when RF 50 times/min. Conclusion：RF slowing down would shift HFP to relatively low frequency，sometimes to LF segment，which would increase LF and decrease HF. Enhanced HRV analysis could exclude this influence.