Depth-related changes in bacterial community structures and functions were analyzed in a paddy soil profile using denaturing gradient gel electrophoresis (DGGE) and a metabolic profiling technique (BIOLOG ECO plates). Canonical correspondence analysis (CCA) was used to analyze the correlations between the relative abundance of bacterial groups and soil-available elements. DGGE and sequencing analysis revealed 12 classes and one unknown bacterial group. At the family level, Comamonadaceae and Moraxellaceae dominated through the soil profile, while Acidobacteriaceae and Nitrospiraceae dominated in the deepest layer. In addition, Streptococcaceae dominated and was only observed in the deeper layers. Metabolic profiles revealed the greatest carbon source utilization capacity in the surface layer, and no significant differences between upper and deeper soil layers. The carbon sources utilized by microorganisms were different among the different layers. CCA indicated that soil-available Mn, Ca, Cu, Al, and K concentrations were positively correlated with the relative abundance of Comamonadaceae, Moraxellaceae, Streptococcaceae, Microbacteriaceae, Nocardioidaceae, and Nitrospiraceae in the profile. The results showed that the paddy soil profile harbored diverse bacterial communities and experienced depth-related changes in community structure and carbon source utilization. The bacterial communities and functions might be shaped by the soil edaphic characteristics along the soil profile.