In this study, by using nanopore direct RNA sequencing, we sequenced the transcriptome and m6A methylation modification of M. coruscus infected with V. alginolyticus and uninfected M. coruscus, respectively, to reveal the regulatory mechanism of m6A methylation on mussel innate immunity. This study will help us to understand the general situation of m6A methylation modification in molluscs and its regulatory role in some life activities.