Understanding of the effects of perturbation strategies on soil microorganisms is helpful in optimizing bioremediation systems and enhancing their efficiency. Four soil mesocosms were constructed for bioremediation of highly polycyclic aromatic hydrocarbon-contaminated soil using the flowering plant Orychophragmus violaceus and/or bacterium Rhodococcus ruber Em1. Bacterial community dynamics were evaluated by 454 pyrosequencing, and Em1 abundance was assessed by quantitative polymerase chain reaction. The results showed that the diversity of the bacterial community increased gradually with time; the degree of increase was in the order mesocosm PE (combination of O. violaceus and Em1), mesocosm WE (Em1), mesocosm PC (O. violaceus only), mesocosm WA (attenuation). Increased diversity may be predictive of PAH degradation. O. violaceus had a marked effect on bacterial community evolution and promoted the growth of Em1. The bacterial community of mesocosm PE gradually separated from the others, as indicated by Venn diagrams and weight-principal component analysis. Abundances of the families Cytophagaceae + Nocardioidaceae + Iamiacaeae (Actinobacteria), and Alcanivoracaceae + Pseodomonadaceae + Xanthomonadaceae (Gammaproteobacteria) were positively correlated with PAH degradation. Our findings help bridge the gap between field bioremediation and laboratory approaches, provide insight into processes of microbial ecological recovery, and will be useful in developing strategies to optimize bioremediation by modifying plant-microbe interaction patterns.