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Simple Summary: In crustaceans, especially economic shrimp and crabs, autotomy significantly affects the survival rate and growth performance. At present, the molecular mechanism of the limb regeneration process of economic crustaceans is rarely studied. In this study, we used the pressure method to remove the pereopods of Exopalaemon carinicauda and recorded the regeneration process in detail. Moreover, regenerated pereopod tissue was sliced and stained with H.E. Microscopic observations revealed significant changes in the type and number of associated cells including outer epithelial cells, granulocytes, embryonic cells, and so on. This study performed a comparative transcriptome analysis of samples from different stages of limb regeneration and identified multiple differentially expressed genes that may be associated with crustacean growth or molting. The sequence and expression characteristics of the innexin gene were analyzed. Our study explored the morphological and molecular changes during limb regeneration of E. carinicauda, and laid a foundation for further research on molecular regulatory mechanisms. With the increase in breeding density of Exopalaemon carinicauda, appendage breakage may occur, which seriously affects survival and economic benefits. To study the limb regeneration process of E. carinicauda, we induced autotomy of the pereopods. After a period of time, wound swelling disappeared, the pigment gradually accumulated, and a tawny film subsequently formed in the wound. The healing period of the wound occurred 24 h after autotomy, and the blastema formation stage occurred 48 h after autotomy. After 4 days of cutting, the limb buds began to differentiate, grow, and expand rapidly, and this process lasted approximately 15 days. Microscopic observations revealed significant changes in the type and number of associated cells including outer epithelial cells, granulocytes, embryonic cells, columnar epidermal cells, elongated cells, and blastoma cells, during the process from limb fracture to regeneration. A comparative transcriptome analysis identified 1415 genes differentially expressed between the J0h (0 h post autotomy) and J18h (18 h post autotomy), and 3952 and 4366 differentially expressed genes for J0 and J14d (14 days post autotomy) and J18h and J14d, respectively. Some of these genes may be related to muscle growth or molting, as indicated by the presence of troponin C, chitinase, actin, innexin, and cathepsin L. As a functional gene involved in epidermal formation, the mRNA expression level of the innexin inx2 in the pereopod of E. carinicauda changed significantly in the experimental groups (p < 0.05). The results of this study contribute to existing knowledge of regeneration mechanisms in crustaceans. [ABSTRACT FROM AUTHOR]