SITE model was developed to study the response of tropical ecosystems according to environmental conditions for estimating of energy fluxes. This study analyzed the net ecosystem of CO2 exchange (NEE) by ecosystem modeling and field measurements in a semi deciduous forest located at 50 km of Sinop municipal district, Mato Grosso, Brazil. Continuous measurements of canopy CO2 storage and fluxes of CO2 were made in a tower of 42 m height using an eddy covariance technique. For ecosystem modeling was used SITE to estimate the NEE. SITE required a setting of parametrization. The better performance of the SITE model to estimate NEE was obtained during the wet season.