To better understand the growth condition of vegetation, our study was conducted to explore the dynamics of the soil bacterial community in the hydro-fluctuating zone of the Three Gorges Reservoir (TGR) region in China. In July (2012, 2013, and 2014). We collected and compared soil samples from under two plant species (Hemarthria compressa and Cynodon dactylon) and bare soil. We characterized bacterial community diversity using the terminal-restriction fragment length polymorphism (T-RFLP) molecular method, and also investigated soil chemical properties. Our results show that (1) bacterial diversity was significantly influenced by plant species, time, and their interaction, regardless of which enzyme was used for digestion (HhaⅠ or MspI); however, species for the Shannon-Wiener index (H) and time for the Simpson index (D) when digested by HhaⅠ did not significantly influence bacterial diversity. (2) The richness index (S) of the planted vegetation was significantly higher than in bare areas. In addition, the S, H, D, and evenness (E) indices were more stable for bacterial communities under planted vegetation than bare areas. (3) Vegetation and sampling times influenced the types and relative abundance of predominant terminal restricted fragments in our study. (4) CCA (canonical correspondence analysis) analysis showed that long fragments were more concentrated, especially around nitrogen and phosphorus, and soil bacterial diversity had a close relationship with chemical properties, such as nitrogen, phosphorus and organic matter. In conclusion, two different enzymes were used to explore the diversity of the soil bacterial community in the TGR region, and their digestion maps, analyzed by synthesis, illustrate that our analysis results are objective. Furthermore, the results indicate that vegetation type and soil chemical properties affect diversity in the soil bacterial community. However, in the fluctuation zone of the TGR, the bacterial diversity indices became more stable after revegetation, which confirms that planted revegetation can improve soil bacterial diversity; in addition, bacterial diversity was affected by soil chemical properties (N, P, OM).