Based on the work of Huang et al. in 1998, an inventory of CH4 emission from rice paddies for China was developed. For the year 2000, the annual total emission is estimated to be 9.26 Tg, and the inventory shows large seasonal and regional variation. With the aid of the mesoscale meteorological model MM5 and the photochemical model CALGRID, the effects of the forenamed natural CH4 emission and the CO emission from biomass burning estimated by Streets et al. on tropospheric chemistry over China were investigated. The results indicate that the countrywide mean surface concentrations of CH4, CO, OH, HO2 and O3 significantly changed. The CH4 emission from rice paddies results in a maximum CH4 increase of 66.97μg•m-3 near the paddy soils. But because of VOC and CO in the air, the natural CH4 emission has little effect on the radicals and O3. So the countrywide mean surface concentrations of O3 and HO2 increase 0.24% and 0.4%, respectively, and OH decreases 0.06%. The CO emission from Biomass burning causes the concentration of CO near the sources increase more than 60μg•m-3. Owning to its effects, the countrywide mean surface concentrations of OH, HO2 and O3 vary -2.2%, 2.8% and 0.9%, respectively. Comparatively speaking, the impact of the CO emission from biomass burning on O3 formation is greater than the CH4 emission from rice paddies. Furthermore, the previously mentioned effects are different here and there in correspondence with the distribution of landuse types. They also vary with the seasons, and the variation is much higher in summer than in any other seasons.