We investigated the effect of forest thinning on soil nitrogen mineralization, nitrification and transformation in a Cryptomeria japonica plantation at high elevation to provide basic data for forest management. We chose four study plots for control, light, medium and heavy thinning treatment, and three sub-plots for buried bag studies at similar elevations in each treatment plot to measure the net N mineralization and nitrification rates in situ. The contents of soil inorganic N (ammonium and nitrate) were similar between treatments, but all varied with season, reaching maxima in September 2003 and 2004. The seasonal maximum net Nmin rates after four treatments were 0.182, 0.246, 0.303 and 0.560 mg·kg−1·d−1 in 2003, and 0.242, 0.258, 0.411 and 0.671 mg·kg−1·d−1in 2004, respectively. These estimates are approximate with the lower annual rates of N mineralization for this region. Forest thinning can enhance net N mineralization and microbial biomass carbon. The percentage of annual rates of Nmin for different levels of forest thinning compared with the control plot were 13.4%, 59.8% and 154.2% in 2003, and 0.1%, 58.8% and 157.7% in 2004 for light, medium, and heavy thinning, respectively. These differences were related to soil moisture, temperature, precipitation, and soil and vegetation types. Well-planned multi-site comparisons, both located within Taiwan and the East-Asia region, could greatly improve our knowledge of regional patterns in nitrogen cycling.