Background and aims <p>Intercropping has been demonstrated to enhance crop productivity and phosphorus (P) uptake, in which root-microbe interactions played crucial roles. Our previous results showed that this beneficial effect of intercropping depends largely on a match between root traits and rhizosphere processes. However, little is known about the role of soil microbial communities in underground processes.</p> Methods <p>Using a long-term field experiment with three P-fertilizer application rates and five cropping systems of maize, we integrated crop productivity, root physiological traits, root morphological traits and microbial amplicon sequencing data.</p> Results <p>Our findings revealed that intercropping significantly enhanced maize crop productivity and P uptake, accompanied by increased plasticity of morphological and physiological root traits compared with monoculture. Additionally, intercropping with different companion crops significantly altered the soil microbial community structure of maize, while P-fertilizer application rates had minimal effect. Network analysis showed that intercropping promoted more complex and stable microbial networks characterized with increased cooperative relationships, relative to monoculture. The relative abundance of keystones enriched in intercropping systems were positively correlated with crop productivity and P uptake, explaining 41.11% of the variation in maize grain yield. Structural equation modeling (SEM) further indicated that keystones enhanced grain yields of maize by inducing carboxylate secretion and fostering more acquisitive root morphological traits.</p> Conclusion <p>Our study elucidates how intercropping optimizes root-microbe synergies to improve P efficiency, highlighting the potential for targeted manipulation of keystone microbial taxa to enhance P acquisition and crop performance in sustainable agricultural systems.</p>