Background. The integrative control of the autonomic nervous system (ANS) may contribute substantially to the multifractal-multiscale dynamics of heart rate variability (HRV) and we recently proposed a method for HRV multifractal analysis at different scales separately (goo.gl/CvCnmN). Aim. To evaluate the HRV multifractal-multiscale structure with our multifractal spectrum in an ANS model of altered integrative regulation with intact cardiac innervation. Methods. We recorded R-R intervals (RRI) for 10 minutes in 14 spinal cord injured (SCI) individuals with lesion below the 12th thoracic vertebra and in 34 matched able-bodied (AB) controls. The SCI group has intact autonomic cardiac and splanchnic control, but altered ANS integrative control. LF and HF powers and LF/HF powers ratio were calculated by FFT. The generalized Hurst coefficients, h(q,tau), with temporal scale tau between 6 and 120 seconds, and q in the range –Q≤q≤Q with Q=4, were calculated by our complexity method. At each scale tau we calculated SD(tau), standard deviation over q of h(q,tau), and the multifractality index MFi(tau) as SD(tau)/(2Q). MFi(tau) represents a temporal spectrum of multifractality, being ≥0 and increasing at scales tau where multifractality increases. Groups were compared by Mann–Whitney test. Results. Spectral powers were similar in SCI and AB groups (LF power: 2.8+0.1 vs 2.8+0.1; HF power: 2.3+0.1 vs 2.2+0.1; LF/HF: 0.56+0.05 vs 0.56+0.06; values in AB vs SCI as mean +SE, with power in ms^2 after Log10 transformation). By contrast, MFi(tau) was lower in SCI individuals at tau <7 s (AB: 0.47+0.12; SCI: 0.29+0.05; median+SE; p<0.05) and around 24 s (AB: 0.22+0.02; SCI: 0.12+0.02; p<0.05). Conclusion. In low-level SCI individuals, the HRV spectrum of multifractality reveals alterations in the ANS integrative control undetected by traditional power spectral analysis and associated with loss of multifractality at specific scales.