Optimal litter size on goat farms is an important trait for production and economic efficiency. The ovary and uterus, key components of the reproductive system, play essential roles in reproductive performance. In recent years, numerous genes linked to goat reproductive performance have been identified. However, reliable marker genes that are specifically associated with litter size require further exploration. In this study, eight Jining Grey goats were divided into high-yield ( = 4) and low-yield ( = 4) groups on the basis of their kidding records to identify key regulatory genes associated with litter size. Ovarian and uterine tissues were collected during oestrus for RNA sequencing (RNA-seq). After two outlier uterine tissue samples were excluded, the remaining 14 samples were subjected to WGCNA and differential expression gene (DEG) analysis. A total of 1224 DEGs were identified (|log2(fold change) ≥ 1|, ≤ 0.05), including 912 in ovarian tissues (monozygotic vs. polyzygotic, MO vs. PO) and 312 in uterine tissues (MU vs. PU). Through WGCNA, we identified 15 coexpression modules, among which four key modules were significantly correlated with litter size. Our analysis focused on the magenta and green modules, as they contained 11 and 3 candidate genes overlapping with the DEGs, respectively. Notably, three genes-, , and -were found to play important roles in both ovarian and uterine tissues. These genes mainly participate in regulatory processes such as RNA polymerase II transcription factor activity, calcium ion binding, and extracellular space organization, highlighting their potential as key candidates for future research. Overall, we identified several gene modules associated with litter size in goats, providing potential molecular markers for investigating litter size traits in Jining Grey goats.