Terrestrial ecosystem are a strong sink of carbon. Forest ecosystem, one of them, has been expected to play an important role in climate changing process by absorbing atmospheric carbon dioxide. On the other hand, agricultural ecosystem that consists mainly of annual crops is regarded as poor contributor to carbon accumulation, because its production (carbon hydrate) is decomposed into carbon at a short period, which is emitted to the atmosphere. However, it is thought that fruit tree plays a great role in decreasing atmospheric carbon dioxide concentration, same as forest. Net ecosystem exchange of $CO_2$ (NEE) was measured to estimate carbon fixation capacity using an eddy covariance (EC) system method in 2 years from 2005 to 2006 at an apple orchard in Uiseong, Gyeongbuk. Average air temperature values were higher in 2006 than in 2005 during the dormant season, and lower by about $5^{circ}C$ over the growing season causing visible cold injuries. Accordingly, we investigated long-term exchange of carbon to determine how much difference of carbon fixation capacity was shown between 2006 and 2005 in terms of environmental and plant variables such as NEE, leaf area index (LAI), and Albedo. NEE was $4.8Mg;C;ha^{-1}yr^{-1}$ in 2005 and $4.7Mg;C;ha^{-1}yr^{-1}$ in 2006, respectively. Low temperature after July in 2006 decreased LAI values faster than those in 2005. Meanwhile, Albedo values were higher after July in 2006 than in 2005. These results show that the low temperature after July in 2006 apparently affected apple growth.