Soil pollution with cadmium (Cd) has posed a threat to our food safety. And rice consumption is the main source of Cd intake in China. Rice intercropping with water spinach is an efficient way for crop production and phytoremediation in Cd-contaminated soil. However, few people work on the Cd remediation by a combination of the passivation and intercropping. In this study, two passivators (the Si–Ca–Mg ameliorant and the Fe-modified biochar with microbial inoculants) were used in the monoculture and intercropping systems to evaluate the potential of co-effect of passivators and cropping systems on the plant growth and Cd phytoremediation. Results showed that the highest rice biomass and rice yield were presented in the intercropping system with the passivator additions, however, relatively lower biomass was showed in water spinach due to the competition with rice. And more Cd accumulated in water spinach while lower Cd in that of different rice parts. The intercropping system with the addition of the Si–Ca–Mg ameliorant and the microbial Fe-modified biochar significantly reduced the Cd contents in brown rice by 58.86% and 63.83%, while notably enhanced the Cd accumulation of water spinach by 32.0% and 22.0%, compared with the monoculture without passivation, respectively. This probably due to the increased pH, the lowered Cd availability in soil, and the reduced TF and BCF values in rice plants with passivator applications. Collectively, this study indicated that rice-water spinach intercropping, especially with the passivator additions, may function as an effective way for Cd remediation and guarantee rice grain safety.