The bio-thermodynamic structures of a mixed native species plantation, a conifer plantation and an Acacia mangium plantation in Southern China were quantified over a period of 15 years based on eco-exergy methods. The efficiencies of structural development and maintenance were quantified through an integrated application of eco-exergy and emergy methods. The results showed that the storage of eco-exergy increased over 3 times in all three plantations, as predicted by the maximum eco-exergy principle. This trend was primarily seen due to the accumulation of biomass, instead of an increase in the specific eco-exergy (eco-exergy per unit biomass), although species richness did increase. The eco-exergy to emergy and eco-exergy to empower ratios of the three plantations generally increased during the study period, but the rate of increase slowed down after 20 years. The dominant trees are the largest contributors to the eco-exergy stored in the plantations, and thus, the introduction of suitable indigenous tree species should be considered after the existing trees pass through their period of most rapid growth or around 20 years after planting. The combined application of C-values and suggested weighting factors in the eco-exergy calculation can imply opposite results, but may also supply useful information for forest management.