Objective To investigate deceleration capacity of heart rate (DC), acceleration capacity of heart rate (AC), and heart rate variability (HRV) in children with hyperthyroidism and the correlations of serum thyroid hormone levels with DC, AC, and HRV. Methods A total of 47 children with hyperthyroidism were enrolled as hyperthyroidism group and 50 healthy children were enrolled as control group. The subjects in the two groups underwent 24-hour ambulatory electrocardiography. The two groups were compared in terms of DC, AC, heart rate (HR), HRV parameters[standard deviation of normal-to-normal RR intervals (SDNN), standard deviation of average normal-to-normal RR intervals (SDANN), root mean square of successive differences between adjacent RR intervals (RMSSD), low-frequency power (LF), and high-frequency power (HF)]. The correlations of thyroid hormone indices[free triiodothyronine (FT3) and free thyroxin (FT4)] with DC, AC, and HRV were analyzed. Results Compared with the control group, the hyperthyroidism group had significantly lower DC, SDNN, SDANN, RMSSD, LF, and HF and significantly higher AC and HR (P < 0.05). In the children with hyperthyroidism, serum FT3 and FT4 levels showed significant negative correlation with DC, SDNN, SDANN, RMSSD, LF, and HF and significant positive correlation with AC and HR (P < 0.05). Conclusions Children with hyperthyroidism have cardiac autonomic nerve dysfunction manifested as reduced vagal tone. Vagal tone decreases with the increasing serum thyroid hormone levels, suggesting an increased risk of cardiovascular disease.