In this study, through farmer surveys and analysis of soil samples collected from fields with varying continuous cropping durations, the causes of garlic continuous cropping obstacles was investigated. Based on the findings, in order to verify the remediation effects and mechanisms of enhancing soil organic carbon (via organic fertilizer application) on reduction of gailic continuous cropping obstacles, a field experiment with three treatments: conventional fertilization (CF, chemical fertilizer only), regular organic fertilizer (OF), and bio-organic fertilizer (BOF) was conducted under equivalent nitrogen, phosphorus, and potassium nutrient inputs. The study explored the impact of organic carbon supplementation on soil active organic carbon fractions, aggregate stability, microbial community structure, garlic Fusarium wilt incidence, and yield. Farmer surveys and soil analysis revealed that in typical fields continuously cropped with garlic for over 15 years, the contents of soil total organic carbon (TOC) and dissolved organic carbon (DOC) decreased with increasing cropping duration. Concurrently, soil compaction, Fusarium wilt incidence, and yield reduction progressively intensified. Garlic yield showed a significant positive correlation with soil TOC and DOC levels. The organic fertilizer application experiment showed that both OF and BOF significantly increased the content of labile organic carbon such as soil dissolved organic carbon (DOC), easily oxidizable organic carbon (EOC), and particulate organic carbon (POC). The proportion of > 2 mm soil aggregates increased to 25.66% and 37.68%, respectively, while the mean weight diameter (MWD) and geometric mean diameter (GMD) increased significantly. OF and BOF increased the copy numbers of soil Actinobacteria, Bacillus, and Pseudomonas, while the abundances of pathogens like Fusarium oxysporum and Fusarium equisetum were suppressed. The content of globularin-related soil protein (GRSP), and the activities of β-glucosidase, dehydrogenase, urease, and alkaline phosphatase were also increased under organic fertilizer treatments. The incidence of root rot was reduced to 18.67% and 15% under OF and BOF, respectively. Compared with CF, the sprout yields under OF and BOF increased by 16.64% and 25.73%, and bulb yields increased by 12.55% and 18.79%, respectively. In conclusion, this study proved that in long-term garlic continuous cropping soils, the loss of soil organic carbon is the important factor for continuous cropping obstacles, applying organic fertilizers can alleviate this obstacle for garlic sustainable production.