American shad (Alosa sapidissima) is a plentiful anadromous spawning fish with a flat side and a spindle-shaped body with a big head and eyes. It is widely distributed in most of the Atlantic and Pacific coasts of the United States and southern Canada, possessing significant economic and ecological value. Due to consumer demand and high economic value, artificially farmed American shad was introduced to China in the early 21st century and quickly cultivated and promoted. Studying early development mechanisms is one crucial way to understand the early physiological and development pathways of fish. Moreover, it can also provide an essential theoretical basis for studying the dynamic changes of fish populations, conducting field resource surveys, and early replenishment mechanisms. However, the early development analysis on American shad has never been studied molecularly. Hence, in the present study, both Illumina sequencing and SMRT sequencing technologies were first successfully employed to analyze the molecular development mechanism of American shad in the early stages of embryonic, larval, and fingerling to provide the foundation for subsequent further studies. The findings provide essential information on understanding the ontogeny and life-history strategies, helping the researchers to develop the breeding, seed production, and culture techniques of American shad in captive conditions.