Objective： A large number of bacteria in infant formula have been inactivated， but they still have adverse effects on the quality and shelf life of products. The traditional pure culture only can detect the viable bacteria， so evaluating the microbial contamination in infant formula by Metagenome strategy is essential and makes up for the disadvantage. Methods： Microbial contamination of six infant formula were evaluated by pure culture， PacBio SMRT （single molecule real-time） and ddPCR （droplet digital PCR）. Results： Coliform groups， Salmonella， Staphylococcus aureus， Enterobacter sakazakii and spores were absent in the infant formula samples by traditional pure culture. A total of 14 bacterial phylum， 138 bacterial genus and 255 bacterial species were identified in infant formula， and psychrotrophic bacteria Bacillus cereus that might affect the product shelf life were at some point present in the infant formula samples， the average relative abundance were up to 23.54%. A low relative abundance of Escherichia coli were detected in the IF3， IF4， IF5 and IF6 infant formula samples， and the relative abundance was 0.06%， 0.01%， 0.15% and 0.05%， respectively. The results of ddPCR showed that the copy numbers after taking the logarithm of Bacillus cereus and Escherichia coli were 5.45 and 4.89， respectively. Conclusion： There were no pathogens were detected in six infant formula， in line with national standards. But Bacillus cereus and Escherichia coli that might affect the product shelf life were at some point present in the infant formula samples. This study combined with multiple technologies to fully assess the microbial contamination in infant formula， establish microbial detection method of infant formula.