Although many studies have reported that microbiota emergencies are deeply involved in the occurrence and subsequent progression of lung diseases, the present diagnosis of lung disease depends on microbiota markers, which is still poorly understood. Therefore, a meta-analysis was performed to confirm lung microbiota markers for the diagnosis of lung diseases. Literature databases were searched following the inclusion and exclusion criteria. There are 6 studies including 1347 patients and 26 comparisons to be enrolled, and then the diagnostic effect was evaluated using Stata 14.0 and Meta-disc 1.4 software. The pooled sensitivity (SEN), specificity (SPE), diagnostic likelihood ratio positive (DLR+), diagnostic likelihood ratio negative (DLR−), and diagnostic OR (DOR), as well as area under the curve (AUC) of microbiota markers in the diagnosis of lung diseases were 0.90 (95% CI: 0.83-0.94), 0.89 (95% CI: 0.76-0.95), 7.86 (95% CI: 3.39-18.21), 0.12 (95% CI: 0.06-0.21), 22.254 (95% CI: 12.83-39.59.14), and 0.95 (95% CI: 0.93-0.97), respectively. Subgroup analysis revealed that research based on Caucasian, adult, BAL fluid, PCR, pneumonia obtained higher AUC values. The microbiota markers have shown potential diagnosis value for lung diseases. But further large-scale clinical studies are still needed to verify and replicate the diagnostic value of lung microbiota markers.