The influence of topographic and biotic factors on forest ecosystem functioning has received more and more attentions in ecology. With the rapid development of DNA barcoding, the phylogenetic relationships of species found in many communities are available, but the role of evolutionary history in determining the ecosystem functioning has not been well explored. In this study, we aimed at understanding the roles of topographic, biotic factors as well as phylogenetic relationships of the species in determining the biomass carbon storage in the 25-ha Baotianman Forest Dynamics Plot (BFDP), Henan, central China. We classified the entire 25-ha plot into 5 habitats based on both topographic and biotic characters. Our results showed that the effective topographic and biotic factors on biomass carbon storage varied among AGBC, BGBC and TBC. Phylogenetic signals were detected for AGBC, BGBC and total biomass Carbon storage. BGBC were more closely related with phylogenetic relationships than others. Our results highlighted the role of evolutionary history in determining biomass carbon storage in different habitats. This will help to understand the underlying the relationship between species diversity and biomass carbon storage, as well as maximizing the carbon storages of local forests in this climate-transition zone.