The antipsychotic drug olanzapine is widely used in the treatment of schizophrenia, bipolar and other mental disorders; however, it causes serious metabolic disorders, including dyslipidemia. Our previous studies have identified that olanzapine activated expression of the sterol regulatory element binding transcription factor 1 (SREBP-1) gene, a key transcriptional factor for lipogenesis in the liver and adipocytes. SREBP-1 has been reported to positively regulate the peroxisome proliferator-activated receptor gamma (PPARγ), a master regulator in the process of adipogenesis. This study aimed to investigate epigenetic modulations of the hepatic PPARγ pathway in olanzapine-induced lipid dysfunctions. Olanzapine led to significant increases of body weight gain, white adipose tissue, fasting triglyceride, and fat accumulation in the liver. A significant upregulation of PPARγ was observed in olanzapine-treated rats. ChIP-deep sequencing showed the increase of H3K4me2 binding on the whole gene loci of key regulators of adipogenesis and lipogenesis, the Pparg, Srebp-1, Cebps families (Cebpa, Cebpb and Cebpd), the Signal transducer and activator of transcription 5 families (Stat5a and Stat5b) and Klfs families (Klf9 and Klf15), as well as muscarinic M3 receptor (Chrm3). ChIP-qPCR revealed that H3K9me3 binding on the promoter of Pparg2 was significantly decreased. Consistently, KDM4B, KDM1A and PHF2, the three histone demethylases responsible for site-specific erasure of H3K9me, was increased in olanzapine-treated rats. These results suggested that olanzapine acted as stimuli to trigger the cascade of adipogenesis and lipogenesis through modulating hepatic histone modifications and subsequently upregulating key transcriptional factors. These findings provided new insight into effective strategies for the prevention and treatment of metabolic side-effects induced by antipsychotic medication.