Background and aims <p>Although water regime and fertilization are known to influence carbon partitioning in the rice–rhizosphere system, how these effects vary across rice growth stages remains poorly understood.</p> Methods <p>We combined ¹³C pulse labeling with soils from a long-term field experiment to trace newly assimilated carbon allocation across rice growth stages under contrasting water regimes and fertilization practices.</p> Results <p>Rice growth stage strongly mediated the effects of water regime and long-term fertilization history on carbon partitioning within the rice–rhizosphere system. Across treatments, most recovered newly assimilated carbon remained in shoots (72–93%). Continuous flooding altered carbon partitioning in a growth stage-dependent manner, promoting carbon allocation belowground at tillering but favoring shoot carbon accumulation during later stages. Compared with mineral fertilization alone, soils with a long-term history of manure application contained approximately 35% more newly assimilated carbon in the rice–rhizosphere system at the tillering stage. They also showed up to twofold greater incorporation of newly assimilated carbon into macroaggregates. Irrigation and fertilization reshaped rhizosphere microbial communities, with water-saving irrigation favoring fungal abundance. These changes were associated with soil nutrient availability, soil organic carbon, and newly assimilated carbon.</p> Conclusions <p>Overall, these findings highlight the role of rice growth stage in mediating the effects of water regime and long-term fertilization on photosynthetic carbon partitioning within the rice–rhizosphere system. Integrating crop developmental stage in irrigation and fertilization management may enhance belowground carbon inputs and increase the potential for soil carbon sequestration while sustaining rice productivity.</p>