A large number of natural shrub forests were converted to oil plants and orchards in the subtropical area of China for economic reasons, but the ecological consequences such as greenhouse gas (GHG) flux, remains unclear. The objectives were to explore how environmental factors, including seasonal and inter-annual variations, and management factors are affecting the GHG fluxes. The study was performed in 18-years-old plantations in a subtropical hilly region in south China. Methane (CH₄), nitrous oxide (N₂O), and carbon dioxide (CO₂) fluxes were continuously measured using a manual static chamber technology at a citrus orchard and Camellia oleifera plantation. Results showed that fluxes of CH₄, N₂O, and CO₂ fluxes were strongly affected by the two plantations, and CH₄ uptake and CO₂ emission rate at the C.oleifera plantation were higher than those in the citrus orchard site mainly due to the high soil temperature and soil organic carbon contents in C.oleifera systems. The citrus orchard had higher annual N₂O emission than the C.oleifera plantation. One of the reasons was N fertilizers were applied to the orchard, as indicated by increase in NO₃⁻-N content and the positive correlation between N₂O emissions and soil NO₃⁻-N. Overall, the global warming potential (GWP) was significantly higher in C.oleifera plantation than that in the citrus orchard (579.11 ± 17.06 vs. 418.13 ± 17.19 kg CO_2eq ha⁻¹ yr⁻¹). The range of annual cumulative fluxes measured from the citrus orchard and C.oleifera ecosystems were – (78.88–92.42) g CH₄–C ha⁻¹ yr⁻¹, 89.3–124.75 g N₂O-N ha⁻¹ yr⁻¹, and 389.58–563.56 kg CO₂-C ha⁻¹ yr⁻¹. The amount of GHG emitted in summer was 1.5–6.6 times higher than the sum of the other three seasons, indicating that CO₂ may be emitted from soil in cool seasons when temperature continues to increase due to global warming. Notably, the continuous increase in the use of fertilizers in economic forests in subtropical hilly regions might increase N₂O emissions, which may offset the net climate benefits of increasing carbon sequestration by plants.