Objective To observe 1~ 15 days of local inflammatory responses after an intramuscular injection of complete Freund’s adjuvant (CFA), clarify the result ing immune response, analyze transcriptomics differences amongst different immune responses, and provide a reference for studies of muscle inflammatory responses. Methods Ninety Wistar rats were randomized into control and model groups at day 1 (MD1), 3 (MD3), 5 (MD5), 7 (MD7), 9 (MD9), 11 (MD11), 13 (MD13) and 15 (MD15) after CFA injection after CFA injection. The 200 μL of CFA was injected in the left femoral biceps abdomen of the mice in the model groups. The changes in mechanical pain and heat pain thresholds were observed in the left hindpaw of mice in each group. The levels of inflammatory factors were measured in the muscle tissue and peripheral blood of each group by electrochemiluminescence. Morphological observations of the local muscle tissue on the injection side of rats in the control, MD3 and MD13 groups were performed using HE staining. The differential expression of genes in the control and model groups was analyzed using genomics. Results ( 1) Intramuscular CFA injection induced sustained mechanical and heat hyperalgesia of the hindpaw. ( 2) At 24 h after CFA intramuscular injection, the levels of IL-6, IL-1β and TNF-α were significantly elevated in the peripheral blood and local tissues, and the pro-inflammatory factor content in the local tissue was significantly elevated again at day 13 after CFA injection. (3) Local tissue was infiltrated mainly by neutrophils on day 3 after CFA injection and mainly by monocytes on day 13 after CFA injection. (4) The differentially expressed genes associated with the immune response are upregulated in local tissues in MD13 group as compared with their levels in MD3 group; These genes are involved in biological pathways related to adaptive immunity, such as Th-cell differentiation and cytokine-cytokine receptor interaction. (5) The expression levels of pain-related genes, including Ccl3, Cxcl1, Cxcl2, Cxcl9 and Cxcl10, were elevated in local tissues after CFA injection. Conclusions An injection of CFA can effectively stimulate innate and adaptive immune responses and induce inflammatory pain sensitization, in which different chemokine family genes play important roles in the different immune responses.