Dichloromethane (DCM) is a harmful volatile organic compound that usually originates from pharmaceutical industry. In this study, the treatment of gaseous DCM in a biofilter was investigated by gradually increasing the DCM inlet concentration. Nearly 80% of DCM could be removed when the inlet concentration was lower than 0.30 g m−3. The maximum elimination capacity of 26.6 g m−3·h−1 was achieved at an inlet loading rate of 38.4 g m−3·h−1. However, with the increase in the inlet concentration to more than 0.60 g m−3, the removal efficiency obviously decreased to about 40%. After a starvation period of 2 weeks, the biofilter rapidly recovered its performance. The Haldane model including a substrate inhibition term was applied to describe the kinetics of the biofilter. High-throughput sequencing indicated that DCM-degrading genera, such as Rhodanobacter sp., Hyphomicrobium sp., Rhizomicrobium sp., Bacillus sp., Pseudomonas sp., and Clostridium sp., were dominant in the biofilter in different operation phases. The microbial communities and diversities were greatly affected by the DCM concentration. Microbial metabolic functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The results indicated that xenobiotics biodegradation and metabolism, carbohydrate metabolism, and amino acid metabolism were the three most abundant metabolic pathways of the microbes. The abundances of these metabolic functions were also altered by the DCM concentration.