The application of nitrogen (N) fertilizer and straw (S) is a common practice in rice cultivation. However, the dynamic changes in the long-term effects on methane (CH₄) and nitrous oxide (N₂O) emissions and soil organic carbon (SOC) and total nitrogen (STN) sequestration rates are poorly documented. A field experiment was performed in the years of 1–2, 6–7 and 12–13 in China with three treatments: no N or S (−N−S), 300 kg N ha⁻¹ without S (+N−S), and 300 kg N ha⁻¹ combined with 4.8 t ha⁻¹ S (+N+S). Compared with −N−S, CH₄ emissions in +N−S varied from a negative effect in years 1–2 (−11.3%) to a positive effect in years 12–13 (7.6%). However, a constant increase was found in +N+S by 3.7, 15.8 and 7.6 times in years 1–2, 6–7 and 12–13, respectively. For N₂O emissions, +N−S relative to −N−S increased by 5.4–8.9 times, and +N+S increased the emissions by from 3.0 to 5.2, and to 17.3 times, respectively. Therefore, the global warming potential (GWP) of CH₄ and N₂O emissions in +N+S was 3.3–3.7, 7.7–14.3 and 5.8–7.8 times higher than that in +N−S and −N−S, respectively. The grain yield of +N+S ranged from 5.6 to 10.0 t ha⁻¹, 30–56% and 42–71% higher than that in +N−S and −N−S. Moreover, the SOC sequestration rates of +N+S decreased from the values of 2.7 to1.6 and to 0.4 t C ha⁻¹ yr⁻¹, respectively, which were 15–80% and 17–73% higher than those of +N−S and −N−S. Compared to −N−S, the +N−S and +N+S increased STN sequestration rates by 0.01–0.06 and 0.03–0.05 t N ha⁻¹ yr⁻¹, respectively. The findings suggest that the positive effects of N and S on the GWP and STN sequestration showed an upward and then downward trend, while the SOC sequestration exhibited a continuous decline.