Multiple cropping systems boost grain yields and have an immense potential to increase land productivity. In such cropping systems in China, soybean is directly seeded after the wheat harvest in early June. After the wheat harvest, the farmland has low amounts of soil moisture and contains large amounts of wheat straw, which negatively affect soybean growth and yields. To address these challenges, an integrated management practice (IMP) than can achieve precise direct seeding and straw mulching return, was developed. In this study, differences in the soil temperature and moisture, seedling quality, dry matter accumulation, soybean yield, and greenhouse gas emissions were investigated between IMP and the farmers’ practices (FP). Compared with the FP treatment, IMP significantly increased the soil moisture and decreased the soil temperature in the topsoil layer. In addition, under the IMP treatment, the rate of emergence and developmental uniformity of soybean plants significantly increased by 21.7% and 99.5%, respectively, thus increasing the leaf area index by 30.0% and dry matter accumulation by 12.0% and, in turn, increasing soybean yields by 24.7%. A principal component analysis showed that the dry matter weight, relative water content, leaf area index, and developmental uniformity were strong sensitivity indices for the IMP treatment. In addition, the intensity of emission of N2O and greenhouse gases under IMP both decreased significantly by 25.1% and 28.9% compared with the FP, respectively. Thus, it was concluded that IMP is a suitable farming practice for sustainable agricultural production, and it has broad prospects for application in wheat–soybean double cropping systems in China and other similar areas globally.