The mechanism of the influence of soil water repellency (SWR) and agglomeration stability on soil organic carbon (SOC) mineralization has not been thoroughly studied following different methods of returning straw to the field. The research background in this study was ordinary black soil, and the addition of straw was accomplished via straw mixing (CT), straw mulching (CM), straw deep burying (CD), and straw tripling deep burial (CE). A 120-day long-term incubation test was used to measure the contact angle between water droplets and soil, the particle size distribution of aggregates and their organic carbon (OC) content, organic carbon pool (OCP) content, OC contribution, and soil CO2-C release, the extent of SWR and the direct effect of agglomerates on SOC mineralization were assessed under different straw return methods. The results revealed that the water-droplet–soil contact angle (CA) was much greater and the rate of CA decline was significantly lower in the CD treatment compared to the CT, CM, and CE treatments, the rate of water droplet penetration on the soil surface was slower, and the SWR was improved. The CD treatment significantly increased the content of macroaggregates and their OCP content, and also significantly increased the content of microaggregates’ OC. The CO2-C emission rate and cumulative emissions were enhanced by adding the same amount of straw, with the most significant enhancement in the deep straw treatment. The cumulative CO2-C emission rate and SOC mineralization significantly increased with increases in SWR, macroaggregates content, and microaggregates OC content, but significantly decreased with increases in macroaggregates’ OC content, according to principal component analysis and Pearson’s correlation analysis. These results highlight the extent of SWR and the direct effect of agglomerate particle size distribution and OC content on SOC mineralization under different straw return methods. This will help to consolidate soil structural stability and nutrient management to support productivity and SOC sequestration in different agricultural systems.