The comprehension of the reciprocal interaction between root development and its co-adapted beneficial microbes in response to elevated CO ₂ (eCO ₂) will facilitate the identification of nutrient-efficient cultivars for a sustainable agriculture. Here systemically morphological, anatomical, chemical and gene expression assays performed under eCO ₂ highlight the divergent root differentiation driven endodermal barrier development with respect to the L-/S-shaped lateral roots under low nitrogen conditions in rice. Next, by metabolome and endodermal-cell specific RNA sequencing we showed that rice adapted to eCO ₂ by spatially recruiting diazotrophs through flavonoid secretion in L-shaped lateral roots. To the end, using a rice Casparian strip mutant Oscasp1-1 we validated such root differentiation driven specific recruitment of a diazotrophic family Oxalobacteraceae implicated in plant tolerance to low nitrogen availability. Our work indicates that rice could coordinate nutrient uptake and root differentiation by the recruitment of diazotrophs in L-shaped lateral roots under climate change.