We aimed to understand how drainage affects structure and functioning of paddy soil microbial communities. Metatranscriptomic libraries were generated from total RNA of both flooded and drained soil. The water potential of the oxic soil was -0.87 MPa after nine days of drainage. RT-qPCR revealed no significant drainage effects on the absolute abundance of bacterial and archaeal SSU rRNA, but fungal SSU rRNA increased significantly. In metatranscriptomics, the relative SSU rRNA abundance of Proteobacteria, Actinobacteria, and Fungi increased, while that of Firmicutes decreased with drainage. Methanogen rRNA was stable, but their mRNA expression and, correspondingly, methane production decreased. As deduced from mRNA analysis, drainage induced proliferation of microbes particularly capable of degrading biopolymers, such as alpha-glucans, lignin and peptidoglycan.