Increasing soil phosphorus (P) availability and plant P uptake are potential approaches to alleviate low P stress in plants and mitigate P resource shortages. Application of fulvic acid (FA) in soil is observed to increase plant growth and P uptake. However, the biological mechanisms underlying these effects remain largely unknown. In this study, based on a three-year field experiment, multi-omics analyses were performed to reveal the effects of FA on rice growth and P uptake, the expression of P transporter genes, root exudates, and rhizosphere bacterial communities in a P-deficient soil. The results showed that FA application significantly promoted rice growth and P absorption under P deficiency, in association with the upregulation of P transporter genes expression and increased rhizosphere P mobilization. FA increased the transformation of non-labile to labile P in the rhizosphere by increasing the secretion of P-dissolving exudates and changing a rhizosphere bacterial community with high P-mobilization capacity, and the variations in the rhizosphere bacterial community were coupled with those of the root exudates, especially glutamylproline, tryptophanamide, 5-chloro-2′-deoxyuridine, L-menthyl (R,S)-3-hydroxybutyrate, and 2,7-diamino-7-iminoheptanoic acid. These findings reveal the multiple positive effects of FA on rice P uptake and indicate the potential utilization of FA in increasing P utilization in rice production.