With an poorly characterized pathogenesis, Diabetic encephalopathy (DE), one of the main chronic complications of diabetes, would require further studies. Recent studies have proven that DE developing in conjunction with neuronal apoptosis, which is tightly regulated by a variety of processes and involved with histone acetylation and molecular signaling or so on. Though the histone deacetylase 4 (HDAC4), HDAC5, HDAC7, and HDAC9 form class IIa of the HDAC superfamily have been found participating in multiple neurodegenerative diseases, while JNK signaling pathway activation was hypothesized as a key cause leading to cell apoptosis, the correlation between HDAC4 and JNK signaling pathway remains unknown. Studies have found that Radix Polygoni Multiflori (RPM) contains a variety of ingredients, such as TSG and Emodin, could exert antioxidant effects, scavenge free radicals, inhibit cell apoptosis and provide neuroprotection, but the underlying mechanism has not fully elucidated yet. In the present study, we further explored the mechanism by which RPM improves the cognitive function of diabetic rats. Simultaneously, TSG and Emodin were used to stimulate HT-22 hippocampal neurons treated with high glucose. After RPM extracts or TSG, Emodin treatments, the cognitive functions of DE rats improved while the hippocampal neurons arranged tighter and increased. Meanwhile, the expression level of HAT, HDAC, HDAC4 and JNK signaling pathway and apoptosis related genes were decreased. Our finds indicates that RPM and Emodin would inhibit HDAC4 expression, curb the activation of the JNK pathway, reduce hippocampal neuron apoptosis and ultimately meliorate the cognitive function from diabetes. Additionally, the markedly inhibitory effects of the RPM and Emodin on HAT and HDAC was identified for the first time in this study, which provides a basis for future drug targeting histones acetylation development and application.