Aims <p>The research intends to investigate the low residual mechanism of Polycyclic Aromatic Hydrocarbons (PAHs) in rice grains across contrasting water management modes in the paddy system. The goal is to understand how varying water conditions affect the accumulation and degradation of PAHs in rice, with the ultimate objective of enhancing the safety and quality of rice grains for consumption.</p> Methods <p>The study was conducted in a paddy system, comparing the impact of distinct water management regimes on PAHs residues in rice grains. It analyzed the activities of functional bacteria and oxidoreductase enzymes in the rhizosphere and evaluated the rhizosphere microbiome network's structural complexity and ecological stability.</p> Results <p>1) Low moisture regulations reduced Phenanthrene (Phe, 22%) and Pyrene (Pyr, 57%) residues in rice grain. 2) Rice, PAHs, and low moisture enhanced network complexity, interactions &amp; functions of microorganisms. 3) Coupling dissipation of Nitrogen (N) reduction and PAHs in Shallow-moist regulated irrigation mode reduced PAHs-residue in rice. 4) Low PAHs, high oxidoreductase activities and habitat suitability ensured rice safety.</p> Conclusions <p>The study concludes that low water regulation not only saves water resources but also improves the stability of the microbial community and the coupling dissipation of PAHs. This reduces the risk of PAHs in paddy fields and maintains the health and safety of rice grains. The findings highlight the criticality of optimizing water management strategies to enhance the quality and safety of rice production.</p> Graphical Abstract <p></p>