Crop straw and N fertilizer applications impact paddy rice yield and greenhouse gas (GHG) emissions. However, their interactive effects have not been well documented. This study investigated the effects of straw (S), no straw incorporation (NS), and three levels of N fertilization rates (N0, N1, and N2) on single rice (SR), double rice (DR), and rice-wheat (RW) cropping systems. Straw incorporation significantly increased total CH₄ emissions by 118.6%, 8.0%, and 79.0% in the SR, DR, and RW, respectively, compared to the NS. The total GHG emissions in DR are significantly 72.6% and 83.5% higher than those in RW and SR, respectively. Compared to NS, straw incorporation significantly increased yield-scaled emissions by 27.8%, 15.0%, and 89.0% in SR, DR, and RW, respectively. Straw with N application significantly increased average rice yield over N1 and N2 by 39.4%, 50.0%, and 6.7% in SR, DR, and RW, respectively. There was a significant correlation between methyl coenzyme M reductase (mcrA) and CH₄ emissions in r_SR = 0.87 (p < 0.05) and r_RW = 0.85 (p < 0.05), except in r_DR = 0.06 (p > 0.05). This study scientifically supports straw incorporation combined with a moderate N application rate in rice-based cropping systems to maintain high rice yields and mitigate GHG emissions.