Phytoremediation has been employed as a cost-effective technique to remove the cadmium (Cd) from soil and water in several ecosystems. However, little is known about whether intercropping the remediating plants with rice (Oryza sativa) crop could reduce Cd accumulation in rice grains. We conducted greenhouse pot and concrete pond trials to explore the effects of intercropping alligator flag (Thalia dealbata, Marantaceae) on soil Cd remediation, paddy soil and microbial properties, and rice production. Our results suggest that intercropping with alligator flag significantly decreased Cd absorption, transportation, and accumulation from the soil to the rice grains (under 0.2 mg kg-1 at a soil Cd content below 2.50 mg kg-1). This decrease was due to the lowered Cd availability and higher soil pH in the rice-alligator flag intercropping system. Although planting alligator flag resulted in the reduction of soil NH4-N and NO3-N, Cd content in the rhizosphere was the main factor restricting microbial biomass, species, and community composition. Alligator flag could tolerate higher Cd contamination, and accumulate and stabilize more Cd in its tissues than rice. Our study suggests that alligator flag intercropped with rice has potential as a phytostabilization plant to produce rice safely for human consumption in moderately Cd-contaminated soils.