Cadmium accumulation in rice is a major source of Cd exposure in humans worldwide. A three-year field experiment was conducted to investigate the ecological safety and long-term stability of biochar combined with lime or silicon fertilizer for Cd immobilization in a polluted rice paddy. The results showed that the application of combined ameliorants could reduce the Cd content in brown rice to meet the Chinese maximum permissible limit for Cd content in food products (0.2 mg/kg). In addition, such amendments stimulated metabolic pathways in soil bacteria, including carbon metabolism, citrate cycle, pyruvate metabolism, biosynthesis of amino acids, and glycolysis/gluconeogenesis, revealing improvements in soil biological activity and soil health. Therefore, the results provide a practical strategy for the safe utilization of farmland with mild levels of heavy metal pollution.