Abstract: In early August 2021, flying squirrels in a compound-toothed flying squirrel farm in Lantian County, Shaanxi Province, suddenly developed the disease of vomiting and coughing, with mucus-like secretions from the mouth and nose, non-stop tumbling and convulsin, with a total mortality rate of 21% and strong contagiousness, which caused huge economic losses to the farmers. In order to diagnose and treat the disease suffered by the compound-toothed flying squirrels in this farm, the experiment was conducted by dissecting the dead compound-toothed flying squirrels, initially identifying the lesion sites and collecting diseased tissue and organ materials. The collected disease material was inoculated in normal agar medium and blood agar medium, and the pathogenic species were identified by molecular biology after isolation and purification, and the pathogenic bacteria isolated were tested for drug sensitivity and treated according to pathogen identification results and drug sensitivity test results. The results showed that the lungs of the compound-toothed flying squirrels were stasis and the respiratory system was damaged on autopsy; the bacterial isolation culture showed gray-white, smooth, moist, round colonies. The PCR product sequencing results showed that the isolates had 99.00% nucleotide similarity with mouse Haemophilus influenzae and 98.21% nucleotide similarity with Mammaliicoccus sciuri; and both pathogens were susceptible to levofloxacin. After the selection of levofloxacin treatment, infectious pneumonia in compound-toothed flying squirrels was effectively controlled and no further mortality cases occurred. The results suggested that the compound-toothed flying squirrels in this farm were infected with bacterial mixed infection pneumonia caused by Haemophilus influenzae and Mammaliicoccus sciuri, and levofloxacin could be used for clinical control in this compound-toothed flying squirrel farm.