Objective To investigate the effect of replacement feeding by amino acid formula (AAF) on intestinal flora characteristics in infants with severe cow's milk protein allergy (CMPA). Methods A total of 23 infants ≤3 months old who were confirmed as severe CMPA and received artificial feeding were enrolled. AAF with the same brand was used to perform feeding intervention. Before intervention and after 3 months of intervention, fecal samples of all infants were collected, and characteristic changes of intestinal flora were evaluated by using the 16S rRNA high-throughput sequencing and bioinformatics analysis. Results Before and after intervention, there were statistically significant differences in Chao1 index, Shannon index, observed species index, Simpson index of intestinal flora between severe CMPA infants (P<0.05), and there was a difference in Beta diversity, as well as the difference between groups was larger than the difference within groups. The results of relative abundance analysis of phylum level and LEfSe analysis revealed that Firmicutes and Bacteroidetes were significantly enriched in intestines of severe CMPA infants after AAF intervention. The results of relative abundance analysis of genus level indicated that after AAF intervention in severe CMPA infants, the relative abundance of Bacteroidetes, Faecalibacterium, and Bifidobacterium in intestines was significantly elevated, whereas the relative abundance of Arcobacter, Klebsiella, Clostridium in intestines was decreased as compared with before intervention; in addition, the results of LEfSe analysis interpreted that Bacteroidetes, Faecalibacterium, Arcobacter, and Klebsiella were marker species with significant difference in abundance. Among the top 10 flora in relative abundance at species level, the relative abundance of Clostridium perfringens, Bacillus acidogenes, Clostridium butyricum, Lactobacillus grigeri, and Lactobacillus reuteri was significantly elevated. Conclusions AAF replacement feeding can increase intestinal flora diversity in infants with severe CMPA, and increase the abundance of Bacteroidetes and Firmicutes, etc.