Greenhouse gases are the main cause of global warming, and forest soil plays an important role in greenhouse gas flux. Near natural forest management is one of the most promising options for improving the function of forests as carbon sinks. However, its effects on greenhouse gas emissions are not yet clear. It is therefore necessary to characterise the effects of near natural forest management on greenhouse gas emissions and soil carbon management in plantation ecosystems. We analysed the influence of near natural management on the flux of three major greenhouse gases (carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O)) in Pinus massoniana Lamb. and Cunninghamia lanceolata (Lamb.) Hook. plantations. The average emission rates of CO₂ and N₂O in the near natural plantations were higher than those in the corresponding unimproved pure plantations of P. massoniana and C. lanceolata, and the average absorption rate of CH₄ in the pure plantations was lower than that in the near natural plantations. The differences in the CO₂ emission rates between plantations could be explained by differences in the C:N ratio of the fine roots. The differences in the N₂O emission rates could be attributed to differences in soil available N content and the C:N ratio of leaf litter, while the differences in CH₄ uptake rate could be explained by differences in the C:N ratio of leaf litter only. Near natural forest management negatively affected the soil greenhouse gas emissions in P. massoniana and C. lanceolata plantations. The potential impact of greenhouse gas flux should be considered when selecting tree species for enrichment planting.