The autonomic nervous system may contribute to the multifractal-multiscale dynamics of heart rate variability (HRV). Aim of this work is to evaluate multifractal-multiscale features of HRV complexity when the integrative autonomic regulation is altered. We recorded R-R intervals for 10 minutes in 14 spinal cord injured (SCI) individuals with lesion below the 12th thoracic vertebra, which have intact autonomic cardiac innervations with partially altered autonomic integrative control, and in 34 matched able-bodied (AB) controls. We calculated powers spectra by FFT and generalized Hurst coefficients, α(q,τ), with scales τ between 6 and 120 seconds and q between -4 and +4, by multifractal multiscale detrended fluctuation analysis. At each scale we calculated α SD(τ) standard deviation of α(q, τ). α SD(τ) is ≥0 and tends to zero at scales where the series is monofractal. AB and SCI groups were compared by Mann-Whitney test. While SCI and AB spectra were similar, α SD(τ) was significantly lower at τ < 7\ s and at τ around 24 s in the SCI group. Thus, in low-level SCI individuals, the HRV multifractal-multiscale detrended fluctuation analysis reveals alterations in the autonomic integrative control, likely due to loss of multifractality at specific scales, that are completely undetected by traditional spectral analysis.