Objectives To observe the difference of gut microbiota in children with asthma at different control levels. Methods Thirty children aged 10 to 12 with asthma were selected from January 2020 to December 2020 and divided into well-controlled group (16 patients) and non-control / partial control group (14 patients) according to the grading standard of asthma control level. Twelve healthy children were selected as the control group. Fresh fecal samples were collected from three group for the detection of 16S rRNA of gut microbiota. Results A total of 30 children with asthma were included. There were 16 cases in the well-controlled group, 10 males and 6 females, aged (12.19±1.11) years; 14 cases in the uncontrolled/partially controlled group, 8 males and 6 females, aged (12.92±1.59) years; and 12 cases in the control group, 6 males and 6 females, aged (13.17±1.03) years. The differences in gender and age among the three groups were not statistically significant (P>0.05). The duration of treatment was (1.22±0.18) years in the well-controlled group and (1.24±0.15) years in the uncontrolled/partially controlled group, with no statistically significant differences (P>0.05). The difference in the absolute value of FEF₅₀ among the three groups was statistically significant (P<0.05). The differences in Alpha diversity index (4 indices) among the three groups were not statistically significant (P>0.05). The relative abundance of Veillonella species in the uncontrolled/partially controlled group was 0.06 (0.01-0.25)%, 0.53 (0.19-0.92)% in the well-controlled group and 0.17 (0.09-0.82)% in the control group, with statistically significant differences among the three groups (P<0.05). A two-by-two comparison revealed that the abundance of Veillonella was significantly lower in the uncontrolled/partially controlled group compared to the well-controlled group as well as the control group, and the difference was statistically significant (P<0.05). ROC curve analysis showed that the area under the curve for the prediction of Veillonella abundance on the level of asthma control was 0.82 (95% CI: 0.66 to 0.98). Conclusions The abundance of Veillonella in the intestinal flora of poorly controlled asthmatic children was significantly reduced, which may be a guideline for the assessment of asthma control level as well as adjuvant therapy.