Diversified cropping systems (e.g., intercropping) can enhance soil health and crop productivity via the integrate utilization of resources, and thus have been recognized as a core strategy for advancing sustainable agriculture and safeguarding long-term security. However, varying row configurations in intercropping systems can directly alter soil properties and crop productivity, and existing research findings remain inconsistent due to differences in experimental sites and agronomic management practices. To address this, a split-plot field experiment was conducted at two sites (Pingdu and Changyi in Shandong, China) to evaluate row configuration effects on soil properties and crop productivity. Treatments included cotton (Gossypium hirsutum L) monocropping (MC), peanut (Arachis hypogaea L.) monocropping (MP), and three intercropping configurations, namely C2P4 (2 rows of cotton intercropped with 4 rows of peanuts), C4P4 (4 rows of cotton intercropped with 4 rows of peanuts), and C4P6 (4 rows of cotton intercropped with 6 rows of peanuts). The results revealed that, on average, compared with monocropping, cotton-peanut intercropping systems demonstrated comprehensive improvements, reducing soil bulk density by 4.2%-15.5%, increasing soil organic matter (5.2%-15.5%), available nitrogen (4.4%-14.1%), and phosphorus (4.7%-12.0%), while enhancing microbial abundance (bacteria: 14.5%-17.4%; fungi: 27.0%-35.7%; actinomycetes: 24.7%-27.3%). Pearson's correlation analysis showed that humus fractions, microbial abundance, and soil nutrient availability are all key determinants of crop yield. These benefits increased progressively with the peanut-to-cotton row ratio. Specifically, the C4P6 configuration (4 rows of cotton intercropped with 6 rows of peanuts) delivered peak performance: cotton and peanut yields reached 4741.65 kgha-1 and 5484.75 kgha-1, respectively, while the soil quality index (SQI) hit a maximum of 1335-an increase of 82.4% compared with monocropping systems. In conclusion, cotton-peanut intercropping enhances crop productivity through optimized root-soil interactions that improve soil structure, nutrient availability, and microbial functionality, with the C4P6 configuration exhibiting superior performance by synchronizing interspecific facilitation. This study provides a practical measure for sustainable agricultural intensification in the Yellow River Basin of China and semiarid regions with analogous soil constraints.