To screen the differentially expressed genes on whole expression profiles of the inflammation-related cytokines in mice infected with influenza virus by the gene chip technology, and to explore the intervention effect of Shufeng Xuanfei Jiedu formula. Male ICR mice were divided into normal group (N group), influenza virus infective model group (M group), Oseltamivir control group (C group) and Shufeng Xuanfei Jiedu formula high, medium and low dose groups (SH, SM, SL groups) according to the random number table method, with 10 rats in each group. A mouse model of influenza virus pneumonia was reproduced by nasal drip of influenza virus strain FM1 (0.05 mL). In N group, 0.05 mL normal saline was used. In SH, SM and SL groups, Shufeng Xuanfei Jiedu formula was used 2 hours after intranasal infection (2 times, equal and 1/2 of the clinical treatment dose, approximately 3.8, 1.9 and 1.0 g×mL-1×d-1) for 4 days. In C group, the dosage of Oseltamivir was 2.5 g×mL-1×d-1. In N group and M group, distilled water was given (0.2 mL once a day). On the 5th day, the whole lung of mice was taken. The lung index was calculated, and the pathological sections were observed. The total RNA of lung tissue was extracted and detected after hybridization with mice whole gene expression spectrum chip to select differentially expressed genes of chemokine pathways. The expression intensity ratio of the chip probe signal in each group vs. M group was calculated, and P < 0.05 and log2ratio > 1 were up-regulated genes, while P < 0.05 and log2ratio < -1 were down-regulated genes. Compared with the N group, the lung index in the M group was significantly higher, and pathological changes were found in lung tissue, which suggested that the model of influenza virus infection was successfully established. Compared with the M group, the lung index of mice in C, SH, SM, SL groups was significantly lower (0.96±0.14, 1.45±0.22, 1.14±0.18, 1.22±0.21 vs. 1.72±0.15, all P < 0.05), and the extent and degree of lesions were reduced, however, there was no significant difference among the groups. Gene chip analysis showed that there were more differentially expressed genes in N group vs. M group, SH group vs. M group, SM group vs. M group, SL group vs. M group. It could be used for further signal transduction pathway screening. Compared with N group, the differential gene expression of chemokine C-C ligands (CCL-3, CCL-5) and chemokine C-X-C ligands (CXCL-9, CXCL-10) in M group were significantly up-regulated [log2 (M group/N group) were 6.64, 3.51, 5.40, 6.64, respectively]. Compared with M group, the gene expressions of CCL-3, CCL-5, CXCL-9 and CXCL-10 were significantly down-regulated in C, SH, SM and SL groups [log2 (C group/M group) were -3.96, -2.26, -3.12, -2.40; log2 (SH group/M group) were -5.57, -2.37, -1.57, -1.01; log2 (SM group/M group) were -4.35, -1.47, -1.26, -1.74; log2 (SL group/M group) were -2.86, -1.86, -1.23, -1.39, respectively]. Shufeng Xuanfei Jiedu formula inhibits inflammatory damage in mice after influenza virus infection by down-regulating the expressions of CCL-3, CCL-5, CXCL-9 and CXCL-10 on chemokine pathways.