Objective This longitudinal study evaluated the long-term efficacy and safety of hematopoietic stem cell transplantation (HSCT) in slowing the progression of CSF1R-related disorder (CSF1R-RD).Methods Six symptomatic patients (mean follow-up, 6.6 years) were compared with six matched, untreated controls. The CSF1R Clinical Severity Score (CCSS), Montreal Cognitive Assessment, and Sundal radiological score were used for evaluation.Results Post-HSCT clinical progression slowed significantly from 14.1 to 3.7 CCSS/year, compared with 15.2 CCSS/year in the control group (p<0.01). Cognitive decline was substantially reduced (-1.5 points/year vs. -7.6 points/year), and radiological deterioration slowed (0.4 per year vs. 3.9 per year). Notably, during the observation period, all HSCT patients survived, whereas 50% of the patients in the control group died. No serious transplant-related complications were observed.Conclusion HSCT is a potent disease-modifying therapy for CSF1R-RD that drastically improves survival and slows deterioration. These findings underscore the necessity of early intervention during the symptomatic phase to maximize the preservation of quality of life for affected individuals.