In order to elucidate the characteristics and variations in rice yield, quality, and economic benefits under different modes of comprehensive rice field planting and aquaculture systems. This study investigated three modes: rice-shrimp (RL), rice-fish (RF), and rice-duck (RC). These were compared with the rice monoculture mode (CK). Results indicate that, compared to CK, three modes significantly increased rice yield. A higher accumulation of dry matter during the main growth stages, a larger LAI, and elevated photosynthetic potential, population growth rate, and net assimilation rate during crucial growth phases. The three modes significantly increased the rice milling yield compared to CK. They increased the content of amylose by 0.90% to 1.29% and improved the protein content by 0.03% to 0.78%. RC demonstrated a more pronounced effect on enhancing the taste quality of rice. Economically, the three modes exhibited a notable increase in economic benefits, ranging from 153.06% to 431.40% compared to CK. This improvement in economic returns was primarily attributed to increased income from aquatic product farming and premium pricing for high-quality rice. In conclusion, the comprehensive rice field planting and aquaculture system represents a stable, quality-enhancing, and efficient rice production method.