Objective. This study is aimed at examining the efficacy of human umbilical cord blood-mononuclear cell (hUCB-MNCs) transplantation through lateral atlanto-occipital space puncture in multiple system atrophy (MSA) treatment and investigating changes in T-cell subsets in peripheral blood and inflammatory factors in patients before and after treatment. Methods. A total of 20 patients with MSA who underwent hUCB-MNC transplantation through lateral atlanto-occipital space puncture in the Liaocheng People’s Hospital were enrolled. Patients were followed up at 0, 1, 3, and 6 months after treatment, and the Unified Multiple System Atrophy Rating Scale (UMSARS) scores, TNF-α in the peripheral blood, IL-6, percentage of CD4, and CD4/CD8 ratio were evaluated and compared for each follow-up point; any adverse effects were recorded. Results. UMSARS Part I scores were , , and , 1, 3, and 6 months, respectively, after treatment and were significantly lower as compared to that before treatment (; ). Similarly, UMSARS Part II scores 1, 3, and 6 months after treatment were , , and , respectively, significantly lower as compared to that before treatment (; ). The IL-6 values in the peripheral blood 1, 3, and 6 months after treatment were , , and , respectively, which were significantly lower () than that before treatment () pg/m. The TNF-α levels at 3 and 6 months after treatment were and , respectively, which were significantly lower than that before treatment (; ). The CD4/CD8 ratios in the peripheral blood 1, 3, and 6 months after treatment were , , and , respectively, which were significantly different than that before treatment (, ). Similarly, the CD4 percentages 1, 3, and 6 months after treatment were , , and , respectively, which were significantly different than that before treatment (; ). Conclusion. hUCB-MNC transplantation through lateral atlanto-occipital space puncture could significantly improve the symptoms and signs in patients with MSA and delay the disease progression. Thus, hUCB-MNCs may modulate immune activity and reduce the inflammatory response.