N6-Methyladenosine (m6A) modification is one of the most abundant post-transcriptional modifications that can mediate autophagy in various pathological processes. However, the functional role of m6A in autophagy regulation is not well-documented duringVibrio splendidusinfection ofApostichopus japonicus. In this study, the inhibition of m6A level by knockdown of methyltransferase-like 3 (AjMETTL3) significantly decreasedV. splendidus-induced coelomocyte autophagy and led to an increase in the intracellularV. splendidusburden. In this condition,Unc-51-like kinase 1(AjULK) displayed the highest differential expression of m6A level. Moreover, knockdown ofAjULKcan reverse theV. splendidus-mediated autophagy in the condition of AjMETTL3 overexpression. Furthermore, knockdown ofAjMETTL3did not change theAjULKmRNA transcript levels but instead decreased protein levels. Additionally, YTH domain-containing family protein (AjYTHDF) was identified as a reader protein ofAjULKand promotedAjULKexpression in an m6A-dependent manner. Furthermore, the AjYTHDF-mediatedAjULKexpression depended on its interaction with translation elongation factor 1-alpha (AjEEF-1α). Altogether, our findings suggest that m6A is involved in resistingV. splendidusinfection via facilitating coelomocyte autophagy in AjULK-AjYTHDF/AjEEF-1α-dependent manner, which provides a theoretical basis for disease prevention and therapy inA. japonicus.