Autistic spectrum disorder (ASD) is a male-biased heterogeneous neurodevelopmental disorder that affects approximately 1%-2% of the population. Prenatal exposure to valproic acid (VPA) is a recognized risk factor for ASD, but the cellular and molecular basis of VPA-induced ASD at the single-cell resolution is unclear. Here, we aimed to compare the cellular and molecular differences in the hippocampus between male and female prenatal mice with ASD at the single-cell transcriptomic level. The transcriptomes of more than 45,000 cells were assigned to 12 major cell types, including neurons, glial cells, vascular cells, and immune cells. Cell type-specific genes with altered expression after prenatal VPA exposure were analyzed, and the largest number of differentially expressed genes (DEGs) were found in neurons, choroid plexus epithelial cells, and microglia. In microglia, several pathways related to inflammation were found in both males and females, including the TNF, NF-κB, Toll-like receptor, and MAPK signaling pathways, which are important for the induction of autistic-like behavior. Additionally, we noted that several X-linked genes, including Bex1, Bex3, and Gria3, were among the male-specific DEGs of neurons. This pioneering study describes the landscape of the transcriptome in the hippocampus of autistic individuals. The elucidation of sexual differences could provide innovative strategies for the prevention and treatment of ASD.