The comprehensive field research on the carbon cycle in forest ecosystem was conducted at Tomakomai Flux Research site (TMK), in a cool-temperate deciduous needle-leaf forest in Hokkaido, Japan. Unfortunately, the tower and observation systems were destroyed by the strong winds during a typhoon in 2004 and the monitoring was stopped. Available datasets are the flux and meteorological data from 2001 to 2003. This dataset is also provided by the AsiaFlux Database (http://asiaflux.net/index.php?page_id=23).