Abstract: A pot experiment was carried out to study effects of the thin-shallow-wet-dry irrigation method on microbial biomass carbon(MBC), microbial biomass nitrogen(MBN), the numbers of nitrification bacteria and denitrification bacteria and enzyme activities in soils at the jointing, booting and milky stages of rice under different nitrogen(N) levels, and to explore variation of soil microbe activities under the irrigation method. There were two irrigation methods, conventional irrigation(CIR) and thin-shallow-wet-dry irrigation(TIR), and three N levels, low N(0.10 g/kg soil), middle N(0.15 g/kg soil) and high N(0.2 g/kg soil). Compared to the CIR treatments, the TIR treatments increase soil MBC by 13%-240%, and decrease soil MBN by 6.5%-47.3%. At the high N level, the TIR treatment increases the number of soil nitrification bacteria at three growth stages slightly, and increases the number of soil denitrification bacteria by 0.7 to 3 times at the milky stage and decreases the number of soil denitrification bacteria by 12.1% to 61.2% at the jointing and booting stages. At the low and middle N levels, the TIR treatments reduce the activity of soil nitrate reductase by 63.8% and 43.3% at the booting stage. Under the same irrigation method, compared to the low N level, the middle N level increases soil MBC and MBN, the numbers of nitrification bacteria and denitrification bacteria, and the activities of catalase, urease and invertase, while the high N level reduces soil MBN and the activities of catalase, urease and nitrate reductase. Thus TIR can effectively improve microbial biomass carbon and the activities of catalase, urease and invertase under the middle N level.