Continuous general anesthesia is able to exert an influence on the related molecules expression in central nervous system. In this study, we established a short time isoflurane inhalation SD rat model to explore the effect of isoflurane on regulating the relative genes expression in hippocampus. Ten-week male SD rats were anesthesia inducted for 30min. We obtained rat hippocampus tissues after anaesthesia on 1st and 3rd day, then reversed transcription of 18 gene expressions before PCR detection. We found that isoflurane could upregulate 6 kinds of gene under different circumstances, Hspd1, Plat, Npr3 were upregulated 1.7 ± 0.2 fold, 1.37 ± 0.1 fold, 1.4 ± 0.2 fold respectively in 1 day after anaesthesia, Thbs4 was upregulated 1.8 ± 0.25 fold in 3 day after anaesthesia and Syp and Mgst1 were upregulated 1.65 ± 0.1 fold and 1.4 ± 0.1 fold in 1d, also upregulated 1.5 ± 0.1 fold and 1.48 ± 0.1 fold in 2 d. Our study showed that isoflurane inhalation anesthesia could upregulate the related gene expression of rat hippocampus, which could influence subsequent expression of the relevant molecular level and the corresponding effect would last for at least 3 days. All these above could provide the basis for clinical application.