A better understanding of the molecular mechanism of intestinal fatty acid absorption could lead to novel approaches to treatment and prevention of fatty acid-related metabolic diseases. Although it is confirmed that absorption of long-chain fatty acids (LCFAs) decreases during the pathological processes, the genetic basis and molecular mechanisms remain largely unknown. N6-methyladenosine (m6A) is the most prevalent internal modification on eukaryotic mRNA. Recently, m6A has been found to play important roles in inflammation and antiviral responses. In this study, we show that deficiency of Mettl3, the core methyltransferase of m6A, exerts antimalabsorption of LCFA activity in vitro through inhibiting the inflammation response mediated by LPS. To substantiate this finding further, we found the levels of triglycerides were also sustained in cells with depleted Mettl3, which were cultured in Transwell to polarize with villus formation to simulate the situation in vivo. Mechanistically, depletion of Mettl3 decreases the m6A level of Traf6 mRNA, thereby its transcripts are entrapped in the nucleus, followed by the decreased expression of Traf6, leading to the suppression of NF-κB and MAPK signaling pathway. Thus, the inflammation response was suppressed, resulting in the sustained absorption of LCFA. Moreover, we found that ectopic expression of Traf6 largely abolishes the sustained absorption LCFA in Mettl3 depletion cells. Collectively, silencing Mettl3 could sustain LCFA absorption through blocking the TRAF6-dependent inflammation response. Our work uncovers a critical function of m6A methylation and provides insight into critical roles of Mettl3 in LCFA absorption and inflammatory disease.