Rodin-B is a selective histone deacetylase (HDAC)-co-repressor of repressor element-1 silencing transcription factor (CoREST) complex inhibitor with an IC50 value of 0.50 μM for the CoREST complex, 0.27 μM for HDAC1, and 0.28 μM for HDAC2. Rodin-B increases the acetylation level of histone H3K9, upregulates the expression of neuron-related genes, thereby promoting the increase in dendritic spine density, the colocalization of synaptic proteins (SV2A and PSD95), and the improvement of hippocampal long-term potentiation (LTP), exerting synaptic protection and repair activity. Rodin-B is promising for research of neurodegenerative diseases related to synaptic dysfunction, especially Alzheimer’s disease.