Objective Based on the theory of homotherapy for heteropathy and mechanisms related to oxidative stress, this study aimed to investigate the protective effect of Chaotian Decoction on hippocampal neuronal injury induced by cyclophosphamide (CTX) in rats. Methods Thirty-two female Sprague-Dawley (SD) rats were randomly divided into four groups: blank control group, model group, high-dose Chaotian Decoction group (14.66g/kg), and low-dose Chaotian Decoction group (3.67g/kg). The model group and each administration group were given intraperitoneal injection of CTX (60mg/kg·d) for 5 consecutive days to establish the injury model, followed by administration of Chaotian Decoction via gavage for 21 days in the Chaotian Decoction groups. Changes in rat body weight were monitored; morphological characteristics of hippocampal tissues were observed using HE staining and Nissl staining; and the levels of 5-hydroxytryptamine (5-HT), γ-aminobutyric acid (GABA), malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) in hippocampal tissues were detected by ELISA. Results Compared with the blank group, the terminal body weight of the rats in the model group was significantly reduced (P<0.05). The arrangement of hippocampal pyramidal cells was disordered, there was a large number of inflammatory cell infiltration, the clarity of Nistenite decreased, some Nistenite bodies appeared nuclear consolidation, the coloration became lighter. The contents of GABA and MDA were significantly increased, and the contents of 5-HT, SOD and GSH-Px were significantly reduced (all P<0.01). Compared with the model group, the high-dose Chaotian Decoction group showed a significant increase in final body weight (P<0.01), more regular arrangement of hippocampal pyramidal cells, reduced inflammatory cell infiltration, and clearly visible Nissl bodies. Additionally, the levels of 5-HT and antioxidant indicators (SOD, GSH-Px) were significantly increased (P<0.05), while the levels of GABA and MDA were significantly decreased (P<0.05 or P<0.01). The low-dose group only showed a significant increase in final body weight (P<0.05) and a decrease in MDA level (P<0.05). Conclusion Chaotian Decoction can ameliorate CTX-induced hippocampal neuronal injury by regulating the oxidative stress pathway (reducing MDA content and increasing SOD/GSH-Px activity) and neurotransmitters (increasing 5-HT level and decreasing GABA level). Its mechanism of action is related to strengthening the spleen, tonifying the kidney, and resisting oxidative stress, which provides new research directions for the treatment of central nervous system injury with traditional Chinese medicine