To explore the colonization characteristics of early intestinal flora in critically ill premature infants and their correlations with clinical effects. Methods A total of 33 critically ill premature infants, whose gestational age was equal or greater than 28 weeks and less than 34 weeks, birth method was Cesarean section, and who received intestinal feeding with formula milk, were selected, and they were assigned to efficacy dissatisfied group (group A, 18 cases) or efficacy satisfied group (group B, 15 cases) according to therapeutic effects. Fecal samples of the two groups were collected within 48 hours after birth, and DNA sequencing was performed on 16S rRNA V3⁃V4 regions of all bacteria in fecal samples by using the Illumina high⁃throughput sequencing technique. The species classification, abundance, and diversity of intestinal flora were analyzed. Results At the phylum level, both groups mainly contained dominant flora in terms of Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and unclassified phylum of bacteria, etc. , moreover, group A exhibited decreased absolute abundance of Actinobacteria and Bacteroidetes as compared with group B (P<0.05). At the genus level, both groups mainly contained dominant flora with respect to Enterococcus, Staphylococcus, Klebsiella, Enterobacte, and Trabulsiella, etc. , in addition, group A yielded decreased absolute abundance of Bifidobacterium, Propionibacterium, Rothia, and Bacteroidetes, whereas an elevated absolute abundance of Enterococcus as compared with group B (P<0.05). The Shannon index and Simpson index of group A were lower than those of group B (P<0.05) ; furthermore, β diversity index analysis revealed that the difference between groups was greater than the difference within groups (R value>0, P<0.05). Conclusion The main dominant flora of intestinal flora in critically ill premature infants with different efficacy are almost the same at the phylum and genus levels, but there are differences in the composition, abundance, and diversity of intestinal flora between critically ill premature infants, therein the absolute abundance of Actinobacteria, Bacteroidetes, and Bifidobacterium, Propionibacterium, Rothia, Bacteroidetes in individuals with unsatisfactory efficacy is decreased, as well as the abundance and diversity of intestinal flora are also decreased.