Objective: To investigate the impact of extracurricular physical activity on heart rate variability (HRV) among primary and secondary school students in Chengdu City, so ao to provide references for scientific exercise prescription. Methods: Using a convenient sampling method, 1 323 primary and secondary students were enrolled from central Chengdu who underwent physical fitness assessments at Sichuan Provincial Institute of Sports Science from September 2020 to January 2022. According to the standards of the National Physical Fitness Monitoring Center, boys and girls were divided into groups with and without extracurricular physical exercise habits. HRV was monitored using the SA-3000P device. Key HRV parameters were evaluated separately by gender, including standard deviation of normal to normal intervals (SDNN), root mean square of successive differences (rMSSD), total power (TP), low frequency power (LF) and high frequency power (HF). Statistical analyses were employed by t-test, Mann-Whitney U-test and Chi square test. Results: lgSDNN, lgrMSSD, TP, LF and HF in the group without extracurricular physical exercise habit [boys:(1.67±0.13)ms, (1.59±0.20)ms, (7.34±0.73)ms 2, (6.11±0.74)ms 2, (6.05±0.87)ms 2; girls:(1.67± 0.13)ms , (1.59±0.19)ms, (7.35±0.60)ms 2, (6.06±0.69)ms 2, (6.12±0.87)ms 2] were lower than those in the group with extracurricular physical exercise habit [boys:(1.75±0.13)ms, (1.72±0.18)ms, (7.69±0.62)ms 2, (6.41±0.76)ms 2, (6.44±0.79)ms 2；girls:(1.73±0.13)ms, (1.68±0.20)ms, (7.60±0.65)ms 2, (6.26±0.86)ms 2, (6.36±0.90)ms 2] ( t =-8.24, -8.75, -6.54, -5.35 , -6.33；-5.10，-4.90，-4.47，-2.71，-2.93, all P ＜0.01). Only the group of boys without extracurricular physical exercise habits showed a decrease in lgLF/HF [0.04(-0.19,0.27)] compared to the group with extracurricular physical exercise habits [ -0.03 (-0.25,0.20)] ( Z=-2.01, P <0.05). When the score classes of autonomic nerve activity, stress index and fatigue index were compared between boys and girls groups without and with extracurricular physical exercise habits, the proportion of boys normal and above scores increased from 79.3%, 84.1%, 71.8% to 91.4%, 95.7%, 87.3%, respectively, and the differences were statistically significant ( χ 2=47.42, 63.66, 38.28); the proportion of girls normal score and above increased from 79.8%, 85.7%, 75.0% to 85.4%, 92.1%, 79.4%, and the differences were statistically significant ( χ 2=48.31, 22.18, 22.22) (all P <0.01). Conclusion The primary and secondary school students who have the habit of extracurricular physical exercise have enhanced compliance in indicators related to HRV, showing more complex heart rate variability.