This study aimed to investigate the relationships between the different levels and degrees of incomplete spinal cord injury (iSCI) evaluated with magnetic resonance imaging (MRI) and the results of non-invasive electromyography (mcsEMG), motor-evoked potentials (MEP), and electroneurography (ENG). With a focus on patients with injuries at four different levels, C3-C5, C6-Th1, Th3-Th6, and Th7-L1, this research delved into the intricate interplay of spinal circuits and functional recovery. The study uses MEP, EMG, and ENG assessments to unveil the correlations between the MEP amplitudes and the MRI injury scores. We analysed data from 85 iSCI patients (American Spinal Injury Association-ASIA scale; ASIA C = 24, and D = 61). We compared the MRI and diagnostic neurophysiological test results performed within 1-2 months after the injury. A control group of 80 healthy volunteers was examined to establish reference values for the clinical and neurophysiological recordings. To assess the structural integrity of spinal white and grey matter on the transverse plane reconstructed from the sagittal readings, a scoring system ranging from 0 to 4 was established. The spinal cord was divided into two halves (left and right) according to the midline, and each half was further divided into two quadrants. Each quadrant was assessed separately. MEP and EMG were used to assess conduction in the corticospinal tract and the contraction properties of motor units in key muscles: abductor pollicis brevis (APB), rectus abdominis (RA), rectus femoris (RF), and extensor digitorum brevis muscles (EXT). We also used electroneurography (ENG) to assess peripheral nerve conduction and to find out whether the changes in this system significantly affect patients' scores and their neurophysiological status. The study revealed consistent positive correlations in iSCI patients between the bilateral decrease of the spinal half injury MRI scores and a decrease of the transcranially-evoked MEP amplitudes, highlighting the complex relationship between neural pathways and functional outcomes. Positive correlations are notably pronounced in the C3-C5, C6-Th1, and Th3-Th6 subgroups (mostly rs 0.5 and above with p < 0.05), while Th7-L1 presents distinct patterns (rs less than 0.5 and p being statistically insignificant) potentially influenced by unique structural compensation mechanisms. We also revealed statistically significant relationships between the decrease of the cumulative mcsEMG and MEP amplitudes and the cumulative ENG scores. These insights shed light on the multifaceted interactions between spinal cord injury levels, structural damage, neurophysiological measures, and motor function outcomes. Further research is warranted to unravel the intricate mechanisms driving these correlations and their implications for enhancing functional recovery and the rehabilitation algorithms in patients with iSCI.