Spinal cord injury (SCI) is a severe condition that often leads to permanent functional impairments. The current treatment options are limited and there is a need for more effective treatments. Human umbilical cord mesenchymal stem cells (hUCMSCs) have shown promise in promoting neuroregeneration and modulating immune response. In addition, miR-124-3p has been identified as a potential biomarker for monitoring the progress of neural repair, making it a focus of the present study, which used a rat model of SCI to evaluate the effects of intrathecal hUCMSC transplantation. The present study included three groups: A sham-operated group, an SCI model group receiving PBS and an SCI group receiving hUCMSCs. Neurological function was assessed using the Basso, Beattie and Bresnahan locomotor rating scale and Rivlin inclined plane test on days 1, 3, 7, 14 and 21 post-injury. Histological analysis included hematoxylin and eosin staining to assess tissue morphology, Nissl staining to evaluate neuron survival and immunofluorescence to detect bromodeoxyuridine (BrdU)+/neuron-specific enolase (NSE)+ cells, which indicate neurogenesis. Detection of brain-derived neurotrophic factor (BDNF) protein expression at various time points in rats with spinal cord injury using western blotting. miR-124-3p expression was quantified using reverse transcription-quantitative (RT-q)PCR to assess its potential as a biomarker for SCI recovery. The hUCMSC group showed significant improvements in motor function compared with the control group, particularly on days 7 and 14 post-injury. Histological analysis revealed reduced scar tissue formation and increased neuron survival in the hUCMSC group. Immunofluorescence analysis showed a higher number of BrdU+/NSE+ cells in the hUCMSC group, indicating enhanced neurogenesis. The expression of the neurorepair-related protein BDNF was markedly higher in the hUCMSCs group compared with the control group. Furthermore, RT-qPCR analysis demonstrated a marked upregulation of miR-124-3p in the hUCMSC group, which was correlated with improved functional recovery. The present study demonstrated that intrathecal transplantation of hUCMSCs notably enhanced recovery following SCI, probably by promoting neurogenesis and modulating miR-124-3p expression. miR-124-3p upregulation in the hUCMSC group highlighted its potential as a biomarker for tracking the progress of SCI recovery. These findings provided a foundation for the future clinical applications of hUCMSCs in SCI treatment and the use of miR-124-3p as a monitoring tool.