As the center of cellular energy regulation in eukaryotic cells, AMPK senses and maintains energy balance in peripheral tissues by modulating various metabolic pathways. It plays a vital role in regulating the body's physiological activities and maintaining the body's homeostasis. Although the AMPK gene family has been extensively studied, systematic identification and analysis of the AMPK gene family in Patinopecten yessoensis are still lacking. In order to understand the characteristics, evolution and biological function of the AMPK gene family in P. yessoensis, we conducted genome-wide identification and functional and evolutionary analysis of the AMPK gene family in P. yessoensis. We also investigated the expression profiling of the AMPK gene family under heat stress. The results showed that three AMPK genes were identified in the genome of P. yessoensis including PyAMPKα, PyAMPKβ and PyAMPKγ, which were necessary subunits to form the AMPK complex. Spatiotemporal expression profiling suggested that three AMPK genes have relatively high expression level before the D-shaped larval stage. The PyAMPKα, PyAMPKβ and PyAMPKγ genes exhibited the highest expression level at the fertilized egg stage, blastocyst stage, and the fertilized egg and 2-8 cell stage, respectively. PyAMPK had distinct expression patterns in various adult tissues with the highest expression in kidney, followed by gill. Furthermore, we found the expression levels of all three AMPK genes in the kidney and gill increased first and then decreased over time in the group under the heat stress. Our study results showed that the AMPK genes not only regulated energy balance at early embryo development in scallops, but also participated in the response to heat stress. This study would benefit for understanding the function and evolution of AMPK gene in molluscs, and laid the foundation for further research on the regulation mechanism in response to heat stress in molluscs.