Abstract: Objective To explore the relationship between heart rate variability (HRV) and deceleration capacity (DC) in children with idiopathic ventricular premature contraction of different origins. Methods The clinical data from 155 children with idiopathic ventricular premature contraction were retrospectively analyzed. According to the age, the children were divided into young children group (< 3 years old), preschool age group (3-6 years old) and school age group (6-16 years old). Each group was divided into the right ventricular type group and the left ventricular type group respectively according to the origin site. The differences of HRV and DC were compared among groups. Results Among three different age groups, the DC and time domain of HRV were significantly different (P all < 0.05). In young children group, RMSSD, HF, LF/HF, DC, and PNN50 were statistically different between right ventricular type group and left ventricular type group (P all < 0.05). In preschool age group, RMSSD, LF, HF, LF/HF, and DC were statistically different between right ventricular type group and left ventricular type group (P all < 0.05). In school age group, the RMSSD, HF, LF/HF, and DC were statistically different between right ventricular type group and left ventricular type group (P all < 0.05). Conclusions Children with idiopathic ventricular premature contraction have impaired regulations of cardiac autonomic system which mainly manifests as reduced tension of vagus nerve. Ventricular premature contraction originated from ventricle preponderance (young children and preschool children are right preponderance while school children are left preponderance) increases the risk of malignant arrhythmia.