Peanut (Arachis hypogaea L.) is an important leguminous oil and economic crop that produces flowers above ground and fruits underground. Subterranean fruit pod development, which significantly impacts peanut production, involves complex molecular mechanisms that likely require the coordinated regulation of multiple genes in different tissues. To investigate the molecular mechanisms underlying peanut fruit pod development, we characterized the anatomical features of early fruit pod development and integrated the snRNA-seq and snATAC-seq data at single-cell levels. Moreover, we identified distinct cell types, such as meristem, embryo, vascular tissue, cuticular layer, and stele cells within the shell wall. These specific cell types were employed to scrutinize potential molecular changes unique to each cell type during pivotal stages of peanut fruit pod development. The snRNA-seq analyses of DEGs (differential expressed genes) unveiled cell-type-specific insights that were not previously discernible through bulk-RNA transcriptome analysis. For instance, MADS-box genes contributing to the formation of parenchyma cells were identified, and gravity-related genes in the vascular cells were detected, indicating an essential role for vascular cells in peg gravitropism. Overall, our single-nucleus analysis provides comprehensive and novel information on specific cell types, gene expression chromatin accessibility during the early stages of fruit pod development. This information will enhance our comprehension of the mechanisms underlying peanut fruit pod development and contribute to efforts aimed at improving peanut production.