The influence of oil palm development on tropical peat soil decomposition rate was investigated by an incubation experiment. Soil samples from soil surface and around underground water table were taken from forest site, and oil palm site at 1st and 9th year after development. The soil samples were sieved into 0–2mm, 2–8mm and 8–20mm and analyzed for carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) fluxes.The development of oil palm did not change the CO2 emissions and showed inconsistent influence on CH4 flux according to aggregate size, while significantly higher N2O emissions were found for aggregates 0–2mm at high moisture of oil palm plantation soils compared with the original forest. Nitrous oxide fluxes showed significant positive correlation with the CO2 flux, which indicated that soil organic matter decomposition was closely related to the N2O production. On the other hand, CH4 flux showed clear emission for aggregates bigger than 2mm, while aggregates size 0–2mm showed consistent CH4 uptake. These results showed that investigation of greenhouse gas emissions in tropical peat soil must take into account the aggregate characteristics of the soil, which are inhomogeneous and mixed with fresh organic matter.