OBJECTIVE: To study the effect of vitamin D (VitD) deficiency on cardiac autonomic nerve function in obese pre-school children. METHODS: A total of 242 pre-school children with simple obesity were enrolled, and according to the serum 25-(OH) VitD level, they were divided into VitD deficiency group (76 children), VitD insufficiency group (83 children), and VitD sufficiency group (83 children). The three groups were compared in terms of deceleration capacity (DC) of heart rate, acceleration capacity (AC) of heart rate, and heart rate variability (HRV). The correlations of VitD level with DC, AC, and HRV were analyzed for the VitD insufficiency and VitD deficiency groups. RESULTS: The VitD deficiency group had the lowest DC, root mean square of successive differences between adjacent RR intervals (RMSSD), and low-frequency power (LF) and the highest AC (P<0.05). The VitD insufficiency group had significantly lower DC, RMSSD, and LF and significantly higher AC compared with the VitD sufficiency group (P<0.05). The VitD deficiency group had significantly lower standard deviation of normal-to-normal RR intervals (SDNN) and high-frequency power (HF) than the VitD sufficiency group (P<0.05). In the VitD deficiency group, VitD level was positively correlated with DC, SDNN, standard deviation of average normal-to-normal RR intervals, RMSSD , LF, and HF and was negatively correlated with AC (P<0.05). In the VitD insufficiency group, VitD level was negatively correlated with AC (P<0.05). CONCLUSIONS: Obese pre-school children with VitD insufficiency or deficiency have cardiac autonomic dysfunction, and cardiac vagal tone decreases with the reduction in VitD level.