Wood CO2 efflux (Rwood) is an important carbon cycling process in forest ecosystems and is less understood in Bornean tropical rainforests compared with that in Neotropics, which have differing biotic and abiotic characteristics. Bornean tropical rainforests have particularly higher aboveground biomass because of high stand densities of tall emergent trees, and no regular seasonal dry period. These properties may reflect specific Rwood variation and higher annual Rwood at the ecosystem scale (annual-Rwood) in Borneo. Hence, in this study, we investigated factors that affect inter-individual variation in chamber-based Rwood on stem surfaces at breast height (chamber-Rwood) and estimated Rwood at the ecosystem scale (ecosystem-Rwood) in a Bornean tropical rainforest. Subsequently, we examined temporal variation in ecosystem-Rwood with environmental factors, estimated annual-Rwood, and then evaluated the effects of large trees on ecosystem-Rwood.Stem growth rates were the most significant predictor of inter-individual variation in chamber-Rwood during all five measurement periods between 2012 and 2014. Accordingly, stem growth rates allowed accurate estimates of ecosystem-Rwood, although chamber-Rwood varied with diameter at breast height (DBH) and tree species in some measurement campaigns. Ecosystem-Rwood decreased with soil moisture. Considering the inter-individual and temporal variation, annual-Rwood was estimated at 7.06±2.09 MgC ha−1year−1. This value was comparable to those determined in Neotropical forests, even though aboveground biomass in the present study site was approximately twice of those in Neotropical sites. Large trees with DBH >70cm comprised 38% of aboveground biomass but accounted for only 23% of ecosystem-Rwood because of the small portion of woody tissue surface area of the large trees. These data indicate that the stand density of large trees can considerably affect aboveground biomass but exert less influence on variation in ecosystem-Rwood among various forests.