The artificial drainage and climate drying induced water table decline has resulted in large peat carbon and nitrogen (C&N) loss in peatlands, however, the effects of water table decline on C&N and microbe dynamics at different peat depths are not clear, as well as the effects of plant change and the restoration effects of rewetting. Here we selected a series of sites from undrained (NP), moderate-drained (MDP), deep-drained (DDP) to rewetted (RP) peatlands to study the variations in plants, C&N sequestration, stable isotopic abundances (δ13C and δ15N) and microbial communities at different depths. We found peatland drainage caused moderate degradation in the plant community, and litter greatly preserved the C&N in the 0–10/20 cm peat. Changes in C&N contents, δ13C and δ15N showed MDP had serious C&N loss in both the surface and part of subsurface peat (0-50 cm), and DDP caused more significant C&N loss in the subsurface peat (30-70 cm) than the surface peat (0-30 cm). Drainage changed the bacterial composition: oligotrophs (Acidobacteria) mostly increased, while copiotrophs (Proteobacteria and Bacteroidetes) mostly decreased. The stronger drainage the severer microbe changes, with serious changes in the subsurface peat rather than the surface peat; bacterial metabolic pathways exhibited similar patterns, and the changed pathways were mostly related to C&N metabolism. Long-term rewetting restored the surface C&N contents, δ13C and δ15N to the NP level with plant and litter recovery, whereas, the C&N contents and most of δ13C and δ15N in the subsurface peat were still significantly different from NP. RP had similar bacterial composition, diversity and metabolic pathways as NP in the surface peat, but the similarities between the subsurface microbes were very low. In addition, the taxonomic change, Shannon and Simpson indices of bacterial communities were significantly correlated with peat C&N dynamics during drainage and rewetting, and there were nine phyla dominantly relating to the peat C&N dynamics. Thus, the drainage caused C&N loss and microbial degradation were closely related, which were hard to be restored in the subsurface peat by the long-term rewetting. These indicated the peatlands with severe drainage or drying may consequently lose the stably restored subsurface C&N for a long-term and may have important implications with respect to climate change.