Partial root-zone irrigation creates a heterogeneous soil moisture distribution that may affect soil microbial biomass and enzyme activity. In order to understand such effect, a pot experiment was conducted to investigate the effects of alternate partial root-zone irrigation (AI) and fixed partial root-zone irrigation (FI) on soil microbial biomass C (MBC), microbial biomass N (MBN) and enzyme activity when conventional irrigation (CI) as the control, under two irrigation levels (normal irrigation and mild water deficit) and two ratios of inorganic to organic N (only inorganic N and combined application of inorganic and organic N fertilizers). Compared to CI, AI increased soil MBC at the jointing stages and urease activity at the tasselling stage, but reduced soil MBC at the bell-mouthed stage, MBN at the jointing and tasselling stages and urease activity at the jointing stage. FI enhanced soil invertase activity at the tasselling stage, but reduced soil MBC and dissolved oxidized C (DOC) at the bell-mouthed stage and MBN at the three stages. Compared to normal irrigation, mild water deficit increased soil DOC at the jointing and tasselling stages, but reduced soil MBC at the bell-mouthed stage and MBN at the jointing stages under AI. Compared to only inorganic N, combined application of inorganic and organic N fertilizers increased soil DOC, MBN and catalase activity at the jointing stage under AI, but it reduced soil MBC and invertase activity at the bell-mouthed stage under FI. Therefore, alternate partial root-zone irrigation increased soil microbial biomass C and dissolved C at the jointing stage under mild water deficit and combined application of inorganic and organic N fertilizers.