Current approaches for treating spinal cord injury (SCI) are mainly based on cell transplantation. Mesenchymal stem cells (MSCs) can help slow the progression of SCI due to their trophic function. However, SCI creates a complex microenvironment that reduces cell activity and hence cellular function, ultimately resulting in poor therapeutic outcomes. To help maintain function in transplanted cells, we produced functional tissue constructs by self-assembly of MSC microtissues comprising of porous gelatin microcarriers (GM) and MSCs. These microtissues maintained cellular activity without incurring an excessive amount of apoptosis and delayed senescence in vitro. The paracrine function of MSCs also improved within microtissues, shown by the increased secretion of nerve regeneration-related factors. Microtissues were transplanted in a rat model of complete spinal cord transection, and therapeutic effects were evaluated through behavioral measurements, imaging, histology, and western blot analysis. RNA-seq of spinal cord tissues using Gene Ontology analysis further revealed that the microtissues may have induced repair in SCI through mechanisms related to neurotrophin-3 (NT-3) regulation of response mediator protein 2 (CRMP2) phosphorylation, and inhibition of inflammatory response through interleukin-17 (IL-17), Chemokine C-X-C motif Ligand 1 (CXCL1) axis. The gelatin microcarrier-based MSC microtissues we developed may be effective in providing a new treatment strategy for SCI.