Objective To explore the molecular connotations of the TCM theory of refraction through theregulating of respiratory diseases and inflammatory bowel disease by Papaver nudicaule L., to analyze the changes of geneexpression in the animal models of the two diseases after treatment, and to reveal their molecular mechanisms in the lungand intestine. Methods The allergic asthma model was established by ovalbumin (OVA) atomization and compared withthe ulcerative colitis model established by the combined immunization. Normal rats were used as controls. After theadministration of Papaver nudicaule L., reverse-transcription polymerase chain reaction (RT-PCR) was used to detect theexpression levels of mRNA of the same differentially expressed genes in lung and intestinal tissues of the two groups of rats.Results Papaver nudicaule L. significantly improved the histological changes in the lung and colon tissues of rats. KEGGannotation analysis results for three key differentially expressed genes, C-C motif chemokine 11 ( Ccl11 ), carbonicanhydrase (Ca) 1, and nuclear receptor subfamily 1, group D, member 1 ( Nr1d1), and the RT-PCR results werebasically consistent with the RNA-sequencing results. Papaver nudicaule L. decreased the expression of C-C motifchemokine 11 mRNA ( P < 0. 05) and increased carbonic anhydrase (Ca) 1 and Nr1d1 mRNA expression in the lung andcolon tissues of both groups ( P < 0. 05, P < 0. 05). Conclusions The lung and intestinal tissues of the rats withrespiratory disease and inflammatory bowel disease have the same differentially expressed genes. Papaver nudicaule L. cansignificantly regulate the levels of differentially expressed genes in the lung and large intestine. This may be a molecularmechanism of Papaver nudicaule L.’s activity to locate the lung meridian and large intestine meridian.