The associations between nutritional markers and heart rate variability (HRV) are poorly addressed. This study aimed to evaluate whether malnutrition is associated with the altered autonomic nervous system (ANS) function. This cross-sectional study was conducted enrolling 175 patients (100 women, mean age 65.1 ± 12.9 years) receiving chronic hemodialysis in a teaching hospital from June to August 2010. We performed HRV measurements before and during the index hemodialysis and compared these HRV values between two groups categorized by the individual nutritional marker. By using the multivariate generalized estimating equation with adjustment, we exhibited the independent associations between HRV and poor nutritional status defined by serum albumin < 3.8 g/dL, total cholesterol < 100 mg/dL, body mass index < 23 kg/m2, bodyweight loss within six months > 10%, bodyweight loss within three months > 5%, and normalized protein catabolic rate < 1.1 g/kg BW/day. The current study disclosed ANS impairment in hemodialysis patients with poor nutritional status. The impaired ANS function might be a potential mechanism linking malnutrition to subsequent adverse prognoses in hemodialysis patients. Further investigations are warranted to confirm these findings and clarify the causal association among this complex issue.