Background: Chronic neck pain (CNP) is a prevalent musculoskeletal condition associated with functional impairment and alterations in autonomic nervous system (ANS) regulation. Heart rate variability (HRV) provides a non-invasive method for assessing autonomic function; however, relationships among HRV indices in individuals with CNP remain insufficiently explored.Objective: To investigate the correlation structure among HRV indices in college students with chronic neck pain.Methods: This cross-sectional observational study included 100 college students aged 18 to 30 years with CNP. HRV was assessed under standardized resting conditions using a validated system during a 5-minute ECG recording. The time-domain parameter RMSSD and frequency-domain parameters LF, HF, and LF/HF ratio were analyzed. Data normality was assessed using the Shapiro–Wilk test, followed by Pearson correlation analysis.Results: Considerable inter-individual variability was observed across all HRV measures. A significant positive correlation was found between RMSSD and HF (r = 0.736, p < 0.01). Moderate positive correlations were observed between RMSSD and LF (r = 0.478, p < 0.01) and between LF and HF (r = 0.583, p < 0.01). The LF/HF ratio demonstrated significant negative correlations with HF (r = −0.330, p < 0.01) and RMSSD (r = −0.417, p < 0.01). Among demographic and cardiovascular parameters, BMI showed a moderate positive correlation with LF/HF (r = 0.244, p < 0.05).Conclusion: HRV indices demonstrated significant interrelationships, with the strongest correlation observed between RMSSD and HF. These findings suggest consistency in autonomic measures among college cadets with CNP and contribute to understanding autonomic regulation in this population. Further controlled longitudinal studies are warranted.