Q fever is a zoonotic disease caused by Coxiella burnetii, which can cause pneumonia, hepatitis, myocarditis, endocarditis and so on, Q fever combined with rhabdomyolysis is relatively rare. Diagnosis of Coxiella burnetii infection is relatively difficult, while high-throughput sequencing, including Oxford Nanopore Technology (ONT) third generation sequencing, can be used as a more sensitive detection method to diagnose Q fever, early diagnosis and timely treatment can generally lead to a good prognosis of Q fever. This paper reports a case of acute Q fever complicated with rhabdomyolysis diagnosed by ONT, patient's condition improved and was discharged from hospital after treatment.