Temperate forest soil is a source of CO₂ and N₂O, and a sink of CH₄, but the effects of thinning and clear-cutting on these GHGs dynamics are not understood well. We monitored GHGs fluxes from soil surface before and after forest management at 14 sites from northern to southern Japan. The soil temperatures at the thinning/clear-cutting plots were relatively higher in summer and lower in winter, possibly due to decrease or absence of canopy cover. No clear changes in soil moisture were observed after thinning/clear-cutting. The CO₂ and N₂O emissions and CH₄ uptake rates increased with increase in soil temperature in all sites. The influence of thinning/clear-cutting was different among the GHGs or sites. In 5 sites subject to thinning/clear-cutting (indicated “*” in the Table), the CO₂ emission rate increased in the two sites with dense understory, while it decreased in the other three sites. This decline in CO₂ emission may result from the decrease in root respiration or organic carbon supply such as litterfall due to fewer understories. The CH₄ uptake rates increased and N₂O emission rates decreased in the cedar sites and CH₄ uptake rates decreased and N₂O emission rates increased in Black Soil (Andisols) sites. Our results suggest that the changes in substrate supply of nitrification rate after thinning/clear-cutting might affect these flux rates. In conclusion, the effect of thinning/clear-cutting on GHGs fluxes in Japanese forest soils has wide variety due to changes in soil temperature and nutrient dynamics in the sites.