Our results show that an increase in planting density by about 50% with a correspondingly reduction in basal N rate by about 30% (DR1 and DR2) enhanced NUE by 14.3–50.6% and rice grain yield by 0.5–7.4% over CK. Meanwhile, DR1 and DR2 reduced GWP by 6.4–12.6% and yield-scaled GWP by 7.0–17.0% over CK. According to the two-factor experiment, soil CH4 production and oxidation and CH4 emission were not affected by planting density