The mechanism of PM2.5 in the air on health is complicated, in which the gut flora may play a role. The work aimed to study the changes of intestinal microflora in PM2.5 inhaled rats, further, to analyze the expression of antibiotic resistance genes (ARGs) in intestinal flora of the rats. The PM2.5 in the air of Fujian Province of China was collected to establish the rat model of PM2.5 inhaled. The fecal samples were sequenced by metagenomic method. Intestinal flora species annotation, common function database annotation and ARGs were analyzed between PM2.5 inhaled rats and normal control rats. The results showed that the number of Firmicutes was significantly decreased while that of Bacteroides was increased in the PM2.5 inhaled rats compared with the control rats at phylum level. In addition, from genus level to species level, the composition of intestinal flora in PM2.5 inhaled group was totally different from those of control group. Especially, PM2.5 exposure can change the expression of ARGs in intestinal flora. The ARGs of rpoB2, Tet44, TetW and TetO increased significantly in the PM2.5 inhaled Wistar rats. Controlling air pollution and reducing PM2.5 emissions are crucial to maintain public health.