Methionine (Met) restriction in the diet can reduce intestinal permeability by modulating the expression of intestinal tight proteins leading to enhance the integrity of the intestinal epithelium. Furthermore, our previous study observed that 2-hydroxy-4-(methylthio)butanoate (HMTBA) increased Tight junction protein 1 (ZO-1) mRNA expression in IPEC-J2 when compared with L-Met. This increment may be related to the decline in RNA N6-methyladenosine (m6A) modification level. Nonetheless, the impact of HMTBA utilization as a source of Met and the effects of combining it with Met restriction on the intestinal epithelial barrier in vivo remains uncertain. We constructed the methionine restrict model and Salmonella typhimurium-induced damage model, and then detected the intestinal damage by real-time qPCR, Immunofluorescence staining, and Elisa, and used LC-MS/MS to detect the m6A level and Met Metabolites. Results exhibited that dietary Met restraint, either through Met or HMTBA as the exclusive Met source, could drastically mitigate intestinal barrier dysfunction and the inflammation caused by S. typhimurium. The underlying mechanism involved in the impact of low HMTBA and Met concentration on intestinal barrier function alteration seems to be associated with changes in Met metabolism, along with m6A RNA or 5-methylcytosine (m5C) DNA level modification. The HMTBA addition to normal levels of Met, apart from enhancing the growth rate, fails to prevent S. typhimurium-induced damage to the intestinal barrier function.