This study examined differences in linear and nonlinear heart rate variability (HRV) parameters in relation to pain intensity in individuals with non-specific chronic low back pain (NSCLBP). Fifty-two participants were classified into two groups based on the Visual Analog Scale (VAS): mild- to-moderate pain (VAS ≤ 7) and severe pain (VAS > 7). Instantaneous R–R intervals (RRi) were recorded at rest, with participants in the supine position, using a digital telemetry system (Polar S810i; Polar Electro Oy, Kempele, Finland). For each participant, a sequence of 256 RRi with the greatest stability was selected and used for both linear and nonlinear analyses. The mean and standard deviation of RRi were calculated, and HRV indices in the frequency domain were obtained. Linear analyses included low frequency (LF) and high frequency (HF) components, while nonlinear analyses comprised symbolic analysis with zero variation (0V%) and two unlike variations (2UV%), Shannon entropy (SE), the Complexity Index (CI), and its normalized form (NCI). The severe pain group showed higher LF and 0V% values and lower HF, 2UV%, SE, CI, and NCI values (p < 0.05). While linear HRV parameters did not show a significant correlation with pain intensity, nonlinear measures—particularly NCI—demonstrated a moderate, significant negative correlation (r = –0.52, p < 0.0. In conclusion, our study shows that higher pain intensity is associated with greater alterations in heart rate variability (HRV). Patients with chronic pain exhibited signs of increased sympathetic dominance, reduced parasympathetic activity, and less adaptable autonomic function, which may influence pain modulation and the body's ability to cope with stress. Furthermore, it was demonstrated that the Visual Analogue Scale (VAS) correlated with HRV variables only in the nonlinear parameters.