The invention relates to a strain marker for assisting COVID-19 diagnosis and application thereof and belongs to the technical field of pathogenic microorganism infection detection. The strain markercomprises at least one of haemophilus parainfluenzae, propionibacterium, veillonella atypica, aggregatibacter segnis, alloprevotellatannerae, campylobacter showae, fusobacteria, fusobacterium nucleatum, fusobacterium periodonticum, gemella sanguinis, haemophilus parahaemolyticus, haemophilus sputorum, porphyromonas gingivalis, prevotella intermedia, prevotella multifurmis, prevotella nanceiensis,prevotella nigrescens and prevotella timonensis. A prediction model ROC obtained by the strain marker has an AUC value being 0.910, and the strain marker can be used for assisting diagnosis of SARS-CoV-2 infection, so that the diagnosing performance on COVID-19 pneumonia can be improved, and the defect that viral nucleic acid detection is false negative can be overcome to a certain extent.