Crop yield is directly influenced by the storage and stabilisation of soil organic carbon (SOC), which is determined by the hydrophobicity of soil humic acid (HA). Changes in soil HA hydrophobicity, humic substances, SOC and crop yield were compared after the application of different amounts of straw returns in the field, and the contribution of straw application in enhancing HA hydrophobicity was examined. The treatments included no straw application and soil stirring, no straw application with soil stirring, application of half-amount straw shallow-mixed field return, application of full-amount straw shallow-mixed field return and application of double-amount straw shallow-mixed field return. Using elemental analysis, infrared spectroscopy and fluorescence spectroscopy, the structural hydrophobicity of soil HA was exhaustively characterised. The results showed that the hydrogen to carbon ratio of HA increased by 11.46 %, the ratio of hydrophobic to hydrophilic intensity increased by 21.02 %, and the ratio of peak B to peak A fluorescence intensity decreased by 32.21 % after 5 years of full amount straw shallow-mixing field return compared to no straw application and soil stirring. The observed results indicate that the augmentation in hydrophobicity stimulates the formation of HA, enhances soil humification, elevates SOC content by 9.78 % and potentially contributes to the ultimate crop yield increase by 22.98 %. Compared with stirring the soil, the contribution rate of applying full amount of straw to increase HA hydrophobicity was 49.57–62.05 %, and the contribution rate to increase SOC and yield were 54.59 % and 76.37 %, respectively. While stirring the soil contributed to increasing hydrophobicity, straw application persisted as the primary factor in enhancing hydrophobicity. The findings of this study have significant implications for understanding the mechanism by which straw improves HA hydrophobicity, thereby facilitating carbon sequestration and increasing crop yield.