A better comprehension of carbon dynamics during agricultural production requires an understanding of the CO2 and CH4 fluxes from an agro-ecosystem after fertilisation. The dynamics of CO2 and CH4 fluxes for plant-soil ecosystems in a ventilated transparent greenhouse were evaluated after a pig manure compost or inorganic fertiliser application at the rate of 150 kg N ha(-1) during Brassica chinensis growth from seedling to maturity. Gas samples for the plant-soil ecosystems were collected using a static chamber approach, and the concentrations of CO2 and CH4 were determined using gas chromatography. The results showed that CO2 was fixed by the plant-soil ecosystem during Brassica chinensis growth after fertilisation and the CO2 and CH4 fluxes were not significantly different among the treatments compared with the control. The ecosystem uptake of CO2 increased with the soil temperature and the variation was in agreement with a first-order exponential curve. The temperature sensitivity of the CO2 efflux at the ecosystem level for the pig manure compost, inorganic fertiliser and control treatments were 7.97, 9.82 and 8.88, respectively. There was a positive correlation between the soil microbial biomass carbon and the CO2 uptake for both fertiliser treatments, whereas the CO2 uptake for the control treatment was increased by the soil microbial biomass nitrogen. The plant-soil ecosystems were minor CH4 sinks and sources, and the CH4 flux ranged from -5.56 to 4.23 mg CH4 m(-2)h(-1) for all of the treatments. The CH4 consumption for the pig manure compost and inorganic fertiliser treatments were negatively correlated with the soil microbial biomass nitrogen, whereas that for the control treatment showed a significant negative correlation with the soil nitrate-N. The results indicate that a plant-soil ecosystem could be a carbon sink, and that fertiliser application had no significant effects on either the CO2 or the CH4 uptake in a plant-soil ecosystem.