Objective To investigate the correlation between the levels of peroxisome proliferator activated receptor (PPARγ) and matrix metalloproteinase-9 (MMP-9) and the intestinal flora of children with mycoplasma pneumoniae pneumonia (MPP) and its diagnostic value. Method A total of 100 children with MPP admitted to Hejian Children's Hospital from January 2021 to January 2023 were collected as the study subjects, according to the course of the disease, they were grouped into an acute phase group (48 cases) and a recovery phase group (52 cases), and 50 healthy children who underwent routine physical examinations in our hospital during the same period were included as the control group, the number of intestinal flora (Escherichia coli, bifidobacteria, Bacteroides, Enterococcus, Lactobacillus) and serum PPARγ, MMP-9 levels were compared among the three groups. Pearson method analysis were applied to analyze the correlation between serum PPARγ, MMP-9 levels and Escherichia coli, bifidobacteria, Bacteroides, Enterococcus, Lactobacillus. Logistic regression was used to analyze the influencing factors of MPP in acute stage and recovery stage. ROC curve was used to analyze the diagnostic value of serum PPARγ, MMP-9 and Lactobacillus levels for acute MPP. Result The numbers of Escherichia coli and Enterococcus and the level of serum MMP-9 in the acute phase group and the recovery phase group were higher than those in the control group, and the acute phase group were higher than that in the recovery phase group (P<0.05); the numbers of Bifidobacterium, Bacteroides, Lactobacillus, and serum PPARγ level in the acute phase group and recovery phase group were lower than those in the control group, and the acute phase group were lower than the recovery phase group (P<0.05). Pearson analysis showed that the numbers of Escherichia coli and Enterococcus were negatively correlated with the serum PPARγ level (P<0.05), there was a positive correlation between the numbers of Bifidobacterium, Bacteroides, and Lactobacillus and the serum PPARγ level (P<0.05); the numbers of Escherichia coli and Enterococcus were positively correlated with the level of serum MMP-9 (P<0.05), there was a negative correlation between the number of Bifidobacterium, Bacteroides, and Lactobacillus and serum MMP-9 level (P<0.05). Logistic regression analysis showed that PPARγ was a protective factor for the development of MPP in acute and recovery stages (P<0.05), MMP-9 was a risk factor for the development of MPP in acute and recovery stages (P<0.05), and Lactobacillus was a protective factor for the development of MPP in acute stage (P<0.05).The AUC of serum PPARγ, MMP-9, Lactobacillus and their combination in the diagnosis of acute MPP were 0.797, 0.761, 0.839 and 0.905, respectively. The sensitivity and specificity of combined diagnosis were 93.24% and 76.34%, respectively. The combination of the three was better than that of serum PPARγ, MMP-9 and Lactobacillus alone (Z Combination of the three-PPARγ=2.604, P<0.001; Z Combination of the three-MMP-9=3.310, P=0.007; Z Combination of the three-Lactobacillus=2.810, P=0.008). Conclusion Serum PPARγ level of MPP children increases with the decreases of Escherichia coli and Enterococcus and the increases of Bifidobacterium, Bacteroides and Lactobacillus, the serum MMP-9 level increases with the increasse of Escherichia coli and Enterococcus and the decreases of bifidobacteria, Bacteroides and Lactobacillus.Serum PPARγ, MMP-9 and Lactobacillus have certain diagnostic value for acute MPP, and the combination of the three has higher efficacy.