Polybrominated diphenyl ethers (PBDEs) are typified as kinds of brominated flame retardants which are widely used around the world. They have some characteristics like semi-volatilization, bioaccumulation, neurotoxicology and endocrine disrupting effects, which severely threaten the ecological system and human health. In this study, a typical aerobic biodegradation strain LB400 was chosen for the performance of degradation kinetics process of lower and middling PBDEs congeners, which are widely detected in the environment. The influence of extra carbon sources as the co-metabolism substrates on degradation performance was discussed. With the simulative computation of variation of thermodynamical state function of key reaction path during degradation, the relationship between the calculated thermodynamics and biodegradation kinetics constant was revealed as well. It is indicated that the highest degradation rate would be obtained if biphenyl were added as the carbon source. Within 0–120 h, all tested PBDEs could be effectively degraded by LB400, and the process could be well described by the first-order kinetics. Relatively, the initial hydroxylation of PBDEs might be the rate-limiting step in the degradation process, and such reactive oxygen radicals as ·OH prefers the nucleophilic addition at ortho/meta position to that occurred at meta/para sites of benzene ring. This study could help deeply understand the molecular mechanics of PBDEs aerobic biodegradation, provide some scientific proofs on the selection of highly efficient degradation strains in the soil as well as the application in the soil contaminated remediation.