This study was aimed at quantification of lysine acetylation and its role in digestive and absorptive function of gastrointestinal tract in response to pigs fed different protein levels. Twelve piglets (Duroc × Landrace × Yorkshire) were weaned at 28 days of age and randomly assigned to two groups with 20% and 17% crude protein (CP) levels with four essential amino acids (Lysine, Threonine, Methine, Tryptophan) in two diets meeting the requirements of weaned piglets. There were no differences between the control (20% CP group) and 17% CP group on the average daily gain (ADG), average daily feed intake (ADFI), and feed gain ratio (F:G). Quantitative lysine acetylome analysis of small intestine showed that, altogether 458 lysine acetylation sites in 293 protein groups were identified. Among these proteins, 307 lysine acetylation sites in 191 proteins groups were quantified. Among these quantified acetylation sites and proteins, eight lysine acetylation proteins are upregulated and six lysine acetylation proteins are down-regulated when compared to the control sample. Their related pathway such as carbon metabolism, glycolysis/gluconeogenesis, biosynthesis of amino acids, pyruvate metabolism, fatty acid metabolism, cysteine and methionine metabolism, antigen processing and presentation, citrate cycle (TCA cycle), mRNA surveillance pathway, fatty acid elongation and glucagon signaling pathway were up-regulated, systemic lupus erythematosus, fatty acid degradation, propanoate metabolism, metabolic pathways, butanoate metabolism, legionellosis, bacterial invasion of epithelial cells, lysine degradation, and apoptosis pathway were down-regulated.