Background and aims: Traditional intercropping of tall and short crops often maintain productivity at the expense of the fitness of the short crop due to planting orientation. There is a need to understand how light interception as influenced by row orientation, affects the vertical allocation of photosynthesized carbon, and how this impacts the rhizosphere microbiota of short crops. This understanding would allow for the optimization of aboveground design to utilize the belowground microbiota for plant and soil health in diversified cropping systems. Methods: We manipulated the row orientation (east-west vs. north-south) of peanut and maize in a field and conducted simulated pot experiment where peanut plants were shaded. By using ¹³C tracer approach and DNA stable isotope probing (DNA-SIP) method, we quantified C allocation by peanuts in its rhizosphere including the rhizosphere microorganisms. Moreover, by combining high-throughput sequencing and bacterial cultivation, we evaluated photosynthesized carbon driven the change of rhizosphere microbial composition and its interaction for fungal pathogen resistance. Results: Field intercropping in the north-south orientation increased peanut photosynthetically active radiation to over two times compared to the east-west orientation. The higher light interception increased the relative abundance of photosynthesized carbon which selectively enriched the rhizosphere biomarker Burkholderia to effectively suppressed the pathogenic fungus Alternaria alstroemeriae. Conclusion: North-south row orientation of peanut and maize intercropping can enhance the allocation of photosynthesized carbon in peanut rhizosphere by changing the light interception. The more photosynthesized carbon triggers the reshape of rhizosphere microbiota and induce beneficial Burkholderia to antagonize peanut pathogen to optimize peanut health.