Residual dibutyl phthalate (DBP) in agricultural soil can be absorbed by crops, posing potential risks to human health through the food chain. Root exudates play a critical role in modulating DBP bioavailability and regulating its uptake, yet the underlying mechanisms remain poorly understood. This study investigated how different root exudates influence DBP absorption dynamics and transport pathways in rice. Citric acid markedly enhanced DBP bioavailability by reducing solution pH and improving root activity through the activation of aquaporin, anion channel, and calcium channels, resulting in higher DBP uptake (bioconcentration factor, BCF = 0.14) and translocation to shoots (translocation factor, TF = 1.66). Conversely, ferulic acid exhibited limited activation, suppressing root activity and hindering DBP uptake and metabolism, which lowered accumulation (BCF = 0.04) and restricted transfer to edible tissues (TF = 0.59). Rhizosphere 16S rRNA sequencing revealed that citric acid selectively enriched acid-resistant Firmicutes, promoting DBP solubilization and accumulation, whereas the control treatment favored Acidobacteria, which facilitated DBP degradation and reduced its availability for root uptake. These findings highlight the pivotal role of root exudates in shaping microbial communities and altering physiological pathways to regulate plasticizer absorption and metabolism in crops, providing novel insights for mitigating phthalate contamination in agricultural systems.