Introduction The autonomic nervous system is crucial in regulating cardiovascular function. Heart rate variability (HRV) analysis, a non-invasive method to assess autonomic function, reflects the beat-to-beat variations in heart rate and provides insights into the dynamic interplay between sympathetic and parasympathetic influences on the cardiovascular system. In this study, we aimed to find the HRV parameters in overweight individuals by comparing different anthropometric parameters, including body mass index (BMI), percentage body fat (%BF), waist circumference (WC), and waist-hip ratio (WHR). Method The descriptive cross-sectional study was conducted on 132 healthy first-year MBBS students (82 males and 50 females), aged between 17 and 23 years. Anthropometric parameters (BMI, %BF, WC, WHR) and HRV were recorded for the participants. The HRV parameters were analyzed for either gender. A student 't' test was used to test the difference between groups BMI <25 kg/m2 and = or >25 kg/m2,and a p-value less than 0.05 was taken to be statistically significant. The Pearson correlation coefficient was used to show the relationship between HRV parameters and BMI, %BF, WC, and WHR as the independent variables. Result A total of 132healthy individuals participated in the study, including 82 males and 50 females. The participants had a mean age of 18.72 ± 0.98 years. Our results suggest that while WC and WHR can be used alongside BMI to indicate sympathetic hyperactivity in males, BMI remains the most significant predictor in females. We found gender-specific differences in high-frequency (HF) related to various anthropometric measures, but these differences were not statistically significant. The low-frequency:high-frequency (LF/HF) ratio exhibits strong positive correlations with all measured anthropometric parameters, suggesting that increased values in BMI, %BF, WC, and WHR are associated with greater sympathetic involvement. Conclusion WC and WHR, alongside BMI, are reliable indicators of heightened sympathetic activity in both males and females. These measures should be utilized to assess healthy individuals for the early diagnosis of dysautonomia, disrupt the cycle of sympathetic overactivity, and prevent cardiovascular complications. All these anthropometric parameters are valuable for indicating sympathovagal balance, making them essential tools in the proactive management of autonomic dysfunction and associated health risks.