With global warming and ban on antibiotics, it occurs occasionally that deoxynivalenol (
DON
) together with
Clostridium perfringens
impairs the gut health of broiler chickens. However, the interactive effect of DON and
C. perfringens
on intestinal health is still unknown. A total of 120 one-day-old Arbor Acres broilers were randomly distributed to 4 groups. Birds were gavaged with
C. perfringens
(8 × 10
8
CFU/d per bird) or sterile medium and fed a DON diet (0 or 5 mg of DON per kg diet) to investigate the interactive effects. The main effect analysis showed that DON diet significantly downregulated (
P
< 0.05) the mRNA expression of mucin-2, B-cell lymphoma-2–associated X, and cysteinyl aspartate–specific proteinase-3 of jejunal mucosa; decreased (
P
< 0.05) the indexes of ACE, Chao1, Shannon, and Simpson; and also decreased the relative abundance of the phylum
Bacteroidete
and the genera
Lactococcus
in jejunal contents of broilers chickens. Meanwhile,
C. perfringens
significantly increased (
P
< 0.05) crypt depth; decreased (
P
< 0.05) the ratio of villi height to crypt depth, the activity of jejunal diamine oxidase, and the relative abundance of
Lactococcus
; and upregulated (
P
< 0.05) the relative expression of B-cell lymphoma-2 and cysteinyl aspartate–specific proteinase-8. Furthermore, the interactions between DON and
C. perfringens
were most significant (
P
< 0.05) in the mRNA expression of lipopolysaccharide-induced TNF factor (
LITA
F
) and
TLR-4
, the abundance of the genera
Lactococcus
in jejunal contents, and butyric acid concentrations in cecal contents of birds. Finally, Spearman correlation analysis suggested that the most negative correlations (
P
< 0.05) with the abundance of the genera except
Lactobacillus
were observed within the mRNA expression of
LITAF
. The abundance of
Lactococcus
had a positive correlation (
P
< 0.05) with the expression of Caspase-3. Most genera except
Lactobacillus
negatively correlated (
P
< 0.05) with acetic acid, butyric acid, and total short-chain fatty acids. In conclusion, dietary deoxynivalenol and
C. perfringens
challenge had a harmful effect on the jejunal health and should be carefully monitored in broiler production.