Dibutyl phthalate (DBP) is widely used as a plasticizer in plastic food packaging and has attracted extensive attention due to its residual hazards and ability to accumulate. Microbial degradation is a very effective way to remove DBP from a polluted environment. In this study, Stenotrophomonas acidaminiphila BDBP 071, a strain that efficiently degraded DBP was isolated from tomato rhizosphere soil. To obtain a comprehensive understanding of the degradation mechanism of DBP by S. acidaminiphila strain BDBP 071, whole genome sequencing of this strain was performed. The results showed that the genome size of BDBP 071 was 3.87 Mb, the G + C content was 69.43%, and the number of predicted coding sequences was 3484. Based on whole genome sequencing, the metabolic pathway related to DBP biotransformation was obtained, and key genes were subsequently verified by a real-time quantitative polymerase chain reaction to infer the degradation pathway of DBP. It was preliminarily predicted that the relative expression of monoester hydrolase of EstB3 is increased in this strain. This study provides a scientific basis for applying S. acidaminiphila BDBP 071 in environmental pollution bioremediation, as well as a rich resource for DBP biodegradation genes.