Background and Aims <p>Sustainable rice production in trace element-contaminated farmlands requires management strategies that simultaneously reduce grain metal accumulation and greenhouse gas emissions while maintaining yield. This study aims to evaluate how different fertilizer types-nitrogen, phosphorus, and potassium-affect these sustainability indicators in a rice-caixin rotation system.</p> Methods <p>A pot experiment was conducted with trace element contaminated soil cultivated with two rice varieties, conventional Xiangzaoxian 45 (<i>Oryza sativa L. subsp. Indica</i>, Rice A) and hybrid Pengyou 1269 (<i>Oryza sativa L. subsp. Indica</i>, Rice B). Two rice–caixin rotation systems (A-G and B-G) were established by alternating Rice A and B with caixin (<i>Brassica rapa var. parachinensis</i> ‘Zengcheng Chicaixin’). The treatments were urea, calcium-magnesium phosphate, potassium chloride and unfertilized control.</p> Results <p>The total zinc concentration in the soil of Rice A was decreased by 41.28% and lead concentration in polished rice of Rice B was decreased by 83.02% and bioaccumulation factors of cadmium and lead were decreased by K. The K treatment resulted in the lowest cumulative carbon dioxide and methane emissions and significantly increased soil carbon sequestration and total system carbon sequestration in Rice A by 108.51% and 93.26%, respectively. Rice B had higher yield and carbon sequestration potential than Rice A.</p> Conclusion <p>Our findings demonstrate that K supports a low-metal, low-emission system with enhanced carbon sequestration, whereas N and P are more conducive to yield improvement. This study provides a fertilizer-specific strategy for achieving sustainable intensification in trace element-affected croplands.</p>