Objective Objective To explore the effect of Jianpi Liqi Formula（JPLQ） on TLR9,NF-κB and iNOS in the duodenum of functional dyspepsia（FD） rats. Methods Thirty six SD male rats were randomly divided into control group,FD model group and JPLQ group of twelve rats in each group. The FD model was established by tail clamping. Then the JPLQ group rats received JPLQ oral administration,while the control group and model group received normal saline. At the end of treatment,the duodenums of rats in each group were excised for the following experiments. The morphology of duodenum was measured by hematoxylin-eosin（HE） staining. The mRNA of TLR9 and NF-κB was tested by Quantitative real time polymerase chain reaction（q PCR）,while the expression of iNOS was revealed by Western blot. Results The morphology of duodenum was normal in each group. The mRNA of TLR9,NF-κB and the expression of iNOS were remarkably increased in model group,and JPLQ treatment were significantly decreased in mRNA of TLR9,NF-κB and expression of iNOS. Conclusion JPLQ could block the TLR9-NF-κB/-iNOS signal pathway to ameliorate the duodenal inflammation,and this may be one of the mechanism underlying the JPLQ formula in treating FD.