[Objective] Aiming at the problems of low soil fertility and difficult organic carbon sequestration in semi-arid sandy areas, this study investigated the effects of different carbon-based biofertilizer combinations on soil structure and fertility in semi-arid sandy environments by adding different biochars and microbial agents.[Method] Five treatments were set up in the study, including organic fertilizer + straw biochar (G) + humic acid + Trichoderma agent (B); organic fertilizer + wood biochar (M) + humic acid + Trichoderma agent (B); organic fertilizer + wood biochar (M) + humic acid + Bacillus agent (Y); organic fertilizer + straw biochar (G) + humic acid + Bacillus agent (Y); and a blank control (CK). The effects of different treatments on soil aggregates and the content of organic carbon fractions were analyzed. [Result] 1) Compared with CK, the soil pH of all biochar treatment groups increased significantly (ranging from 7.66 to 8.39), with the G+B treatment showing the highest pH (8.39). The G+B treatment had the highest carbon-to-nitrogen ratio (close to 14:1), and significantly increased the contents of particulate organic carbon (POC) and mineral-associated organic carbon (MAOC). The ratios of POC to soil organic carbon (SOC) and MAOC to SOC were 1.08 and 0.14, respectively. 2) The G+B treatment significantly improved the soil aggregate structure, with a mean weight diameter (MWD) of 0.43 mm, which was 30% higher than that of CK. The organic carbon content of macroaggregates (>0.25 mm) was 2.60%, significantly higher than that of microaggregates. 3) Compared with CK, the crop yields of the four treatment groups all increased significantly. Among them, the G+B and M+B treatments had relatively higher yields, reaching 3562.9 kg/ha and 3108.1 kg/ha, which were 73.7% and 51.6% higher than that of CK, respectively.[Conclusion] The G+B combination can effectively improve soil structure, enhance carbon pool quality and crop yield in semi-arid sandy areas, and is an optimized soil amendment combination with both carbon sequestration and yield-increasing potential.