Calipash is a special connective tissue on the carapace posterior margin of Chinese Soft-Shell turtle (Pelodiscus sinensis), which is closely related to the stress resistance and nutritional value deposition of P. sinensis. However, previous studies lack knowledge about calipash development, thus its developmental regulation mechanisms are still unclear. In this study, transcriptomics and proteomics analysis of calipash at TK17-TK19 embryonic stages of P. sinensis were used to explore the mechanisms that regulate calipash development. Function analysis of DEGs and DEPs revealed that PI3K-Akt and TGF-beta signaling pathways were significantly related to calipash development. The gene knockdown experiments further validated the regulatory mechanisms of two pathways in calipash development. Results revealed that the PI3K-Akt and TGF-beta signaling pathways jointly participate in regulating the proliferation of calipash cells and the type I collagen anabolism. Our results provided novel insights for understanding of the developmental regulation mechanism of the P. sinensis calipash tissue.