The composite filler micro-embedded with Pseudomonas putida (P. putida) was prepared and the biodegradation performance of the filler was evaluated in a biofilter. Five phases were set up to evaluate the performance of the biofilter under different toluene inlet loadings and transient shock loadings. In particular, the microbial community structure in the biofilms and fillers was measured by sequence analysis of the 16S rRNA gene. The results show that the biofilter packed with the composite fillers was suitable for the biodegradation of toluene. The biofilter could start up quickly with high removal efficiency (RE), and remain above 90 % RE when the empty bed residence time (EBRT) was 18 s and the inlet loading rates were not higher than 41.4 g/(m(3).h). Moreover, the biofilter could tolerate substantial transient shock loadings. The high removal efficiency and elimination capacity contributed to rich bacterial communities for the efficient degradation of toluene. The dominant microbial communities at the phylum level were mainly Firmicutes, Actinobacteria and Proteobacteria. It is noteworthy that the abundance of Bacteroidetes at phylum level and Chungangia and Stenotrophomonas at genus level increased significantly during the re-start period.