Small peptides are more energy-saving and efficiently absorbed compared to amino acids. Our study aimed to evaluate the effect of the Lys-Lys dipeptide on the improvement of growth performance, amino acid metabolism, and gut development in suckling piglets. Twenty-eight newborn suckling piglets were orally administrated with 0.1%, 1%, and 5% Lys-Lys dipeptide for 21 days. Our results showed that the Lys-Lys dipeptide has no significant effect on growth performance and intestinal morphology compared with the control group. We also found that the 1% Lys-Lys dipeptide significantly increased the concentrations of serum Lys, Thr, Phe, and Pro while decreasing Cys compared to the control group. Similarly, the 5% Lys-Lys dipeptide markedly increased the concentrations of serum Lys, Iso, Thr, Asp, Glu, and Pro compared to the control group. Moreover, the Lys-Lys dipeptide downregulated the expression of jejunal Slc7a1, Slc7a2, and Slc15a1 and ileal Slc7a2. Additionally, the Lys-Lys dipeptide decreased the microbiota richness indices and relative abundance of Bacteroidales. In this study, we found that the Lys-Lys dipeptide contributes to the metabolism of amino acids but failed to affect the growth performance of piglets. Additionally, the Lys-Lys dipeptide decreased the relative abundance of Bacteroidales. These results provide a theoretical for the future application and research of Lys-Lys dipeptide in intestinal development of suckling piglets.