BACKGROUND: The cardiovascular autonomic neuropathy (CAN) prevalence is rapidly growing in all populations worldwide. This study aimed to evaluate the reference values for the short-term heart rate variable (HRV) and estimate CAN prevalence in our cross-sectional dataset. METHODS: We conducted a large-scale, community-based, cross-sectional study in a Chinese population. Of 2,092 subjects available for data analysis, 371 healthy subjects were selected to reference the values for the short-term HRV. The short-term HRV analysis was performed for all subjects using a computer-aided examination and evaluation system for spectral analysis to investigate changes in autonomic regulation. RESULTS: In the total sample, the reference value for total power was more than 356.13 ms(2). The cutoff points of 55.45 and 36.64 ms(2) were set for low frequency (LF) and high frequency (HF), respectively. The cutoff points of LFn and HFn were 6.40 and 4.83 nu, respectively. The normative reference of LF/HF ranged from 0.3 to 6.5. Using HRV test (model 1), the estimated age-adjusted CAN prevalence in the total sample was 16.83 %. The estimated age-adjusted CAN prevalence values were 31.07, 21.97 and 20.81 % in DM, HT, and MS patients, respectively. CONCLUSION: Our findings provided reference values for short-term HRV. The estimated CAN prevalence was high in the Chinese population.