Application of bio-fertilizer can improve soil fertility and retard the soil degradation. Based on a field experiment, the changes of soil organic C, aggregate stability and organic C in aggregate fractions were analyzed to investigate the effects of bio-fertilizer (BF) combined with a reduced chemical fertilizer. Bio-fertilizer was applied at rates of 0 (BF0), 30 (BF30), 50 (BF50) and 70 (BF70) t ha-1 and soil samples were collected from 0-20 cm layer in 2018 and 2019. Soil cores were separated into three aggregate sizes (>0.25 mm, 0.053-0.25 mm and <0.053 mm) using the wet sieving method. The highest soil organic C and water soluble organic C were measured in BF70, while BF50 had the highest concentrations of microbial biomass carbon, extractable organic C and KMnO4-C. Significant increases of mean weight diameter (3.16 mm in 2018 and 3.39 mm in 2019) in BF50 compared with BF0 showing the improved soil structural stability after bio-fertilizer application. Increased with increasing bio-fertilizer application rates then remained relative stable, organic C in aggregate fractions was highest in BF50. More organic C was accumulated in aggregates of 0.053-0.25 mm in bio-fertilizer amended soils, suggested that C was mainly occluded in micro-aggregate and benefit for protection of C from microbial decomposition. Our results indicated that bio-fertilizer combined with chemical fertilizer was effective in increasing organic C and its labile fractions, which promoted soil structural stability in turn, thereby improving soil quality.