Soil heavy metal contamination is an increasingly urgent problem throughout the world. Phytoremediation is a cost-effective and ecologically friendly in situ method for the remediation of heavy metal contaminated soils. Rice has the potential for use in soil remediation due to its high biomass production, however, risks related to food safety and low accumulation potential exist. Therefore, in the current study, rice stubble was used as the adsorbent in a modified rice-fish system (MRFS) to assess its accumulation capacity in a model paddy field dosed with 0–40.0 mg kg−1 Cd. The weighted mean concentration (WMC) of Cd in rice stubble increased from 0.498 to 36.365 mg kg−1 to 1.038–71.180 mg kg−1 from 0 to 60 days post-harvest (dph), and the corresponding increment rate was 107.68%, 117.42%, 157.77% and 95.73%, respectively. Sixty-days post-harvest, removal rate of Cd from contaminated soils was 1.11–1.40%, which was greater than that of the Cd-hyperaccumulator Thlaspi caerulescens. The WMC of the heavy metals Cd, Zn, Pb, Cr and Cu in rice stubble increased 51.11–97.50%, and removal rate was 1.93–2.66%. Overall, rice stubble had a high capacity of heavy metal accumulation, mainly benefiting from the synthesis effects of MRFS and the changes of accumulation mechanism within the plant from being alive until death. Notably, this study also provides a new idea for in situ, herbage-based phytoremediation of heavy metal-contaminated soils.