For infants with weakened immune systems, formula milk and complementary foods are the primary sources of nutrition. However, the presence of various potential pathogenic microorganisms in infant foods and their supply chains poses significant challenges to the safety of these products. Therefore, this project utilized whole genome sequencing (WGS) technology to obtain sequencing data from 235 bacterial strains isolated from infant formula (PIF), the formula milk supply chain (PIF chain), complementary foods (CF), and the complementary food supply chain (CF chain). These strains were previously unidentified by MALDI-TOF-MS.