Aims <p>The integration of maize stover waste recycling and organic substitution has been extensively implemented to enhance spring maize yield and ameliorate soil quality in rain-fed agricultural areas. Nonetheless, the intricate mechanisms of plant-rhizosphere microorganism interaction remain poorly understood.</p> Methods <p>This study employed a comprehensive two-year field experiment to elucidate the dynamics of rhizosphere microbiome-plant interactions under stover and organic substitution strategies on the Loess Plateau, facilitated by high-throughput sequencing and carbon and nitrogen composition analyses.</p> Results <p>The findings revealed a significant enrichment in the content of rhizosphere carbon and nitrogen components, with the plant height, yield, and harvest index of spring maize increasing by 2.56%, 5.19%, and 2.67%, respectively, compared to the chemical fertilizer. The dataset, encompassing the rhizosphere microbiome and soil moisture and carbon components, exhibited a strengthened correlation following stover recycling. Concurrently, the rhizosphere bacterial community matrix of spring maize correlated with dissolved organic nitrogen and soil organic carbon in the nutrient matrix by altering carbon and nitrogen cycle pathways upon stover incorporation. Phylogenetic null model calculations demonstrated that prolonged stover recycling mitigated the processes of dispersal limitation and homogeneous selection in rhizosphere fungal communities, with their formation and maintenance predominantly reliant on stochastic events rather than species’ adaptive traits. The rhizosphere microbial co-occurrence network analysis indicated that stover recycling exerted a more pronounced effect on enhancing positive connections within the fungal network compared to the bacterial network.</p> Conclusions <p>Collectively, our findings offer profound insights into the rhizosphere soil microbial interactions with spring maize in rain-fed agricultural areas.</p>