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Biomass heat storage is important for promoting energy closure in forest ecosystems; however, this issue is often ignored in surface energy budgets. To determine an accurate approach to calculate biomass heat storage, we monitored the stem temperature of Pinus sylvestris in different heights, depths and orientations. At the same time, air sensible and latent heat storage and soil heat storage are also monitored together with biomass heat storage to study the heat storage share in surface energy budgets. The results showed that (1) temperature in different heights, depths and orientations in stem showed obviously differences dynamics, and time lags are existed between different measuring points inside stem. (2) Tree biomass heat flux varied around 12 W m−2. Soil heat flux and air heat storage were around 20 W m−2 and 8 W m−2 separately, but out of phase with biomass heat flux. (3) Total heat storage in soil, biomass, and air was 60 W m −2 , accounting for ~10% of net radiation, which is a significant proportion of the total energy flux. This study will help improve biomass heat storage models and contribute to fundamental knowledge regarding energy balance closure in forest ecosystems.