[Objective] To study changes of piglet’s jejunum pathology and jejunum flora caused by porcine circovirus 2 type (PCV2) infections. [Methods] The viremia of three piglets infected with PCV2 by oral and intramuscular injection was determined. Then six weaned pigs, being randomly divided into PCV2 infected group and the control group (n=3), were infected with PCV2 with the same route of infection. The three piglets of each group were slaughtered at 21 d after infection. Jejunum and its contents were collected for microscopic pathology and flora sequencing. [Results] The virus loads of the piglets’ serum achieved a higher level at 21 d after PCV2 infection. The jejunum villous of piglets in the infection group atrophied and fell off. The microbial species and abundance in these jejunums changed, and jejunum flora diversity increased, including the significant decrease of Lactobacillus content and the significant increase of Pseudomonas genus content. [Conclusion] PCV2 infection results in certain changes in piglet’s jejunum flora. A decline in the jejunum beneficial bacteria and the increase of harmful bacteria may further aggravate the piglet jejunum inflammation.