Background The 1-year survival rate of patients on prolonged mechanical ventilation was 29-42% before 2000. By 2012, Carson reported the 1-year survival rate of prolonged mechanical ventilation patients was 52%, an unsatisfactory improvement in survival time. We explored the long-term survival rate of prolonged mechanical ventilation patients at our hospital, 2012-2017. Methods We analyzed retrospectively data from our respiratory care center patients to investigate the discharge status, long-term survival rate, and cause of death. We also compared the 5-year survival rates of prolonged mechanical ventilation patients and our hospital lung cancer patients. Results Five hundred seventy-four patients were admitted to respiratory care center during the study period. The long-term follow-up data of 403 prolonged mechanical ventilation, including 186 patients died in the hospital, 157 discharged prolonged mechanical ventilation patients, and 60 respiratory care ward patients until October 30, 2018. The 1-year survival rate of all prolonged mechanical ventilation patients, discharged prolonged mechanical ventilation patients, and respiratory care ward patients were 24.3%, 50.3%, and 31.7%, respectively. The 5-year survival rates of all prolonged mechanical ventilation patients, discharged prolonged mechanical ventilation patients, and respiratory care ward patients were 18.1%, 40.05%, and 11.7%, respectively. Successful weaning from mechanical ventilation was a key factor in the long-term survival of prolonged mechanical ventilation patients. The 5-year survival rate of discharged prolonged mechanical ventilation patients was better than that of all lung cancer patients. The 5-year survival rates of all prolonged mechanical ventilation patients and respiratory care ward patients were similar to that of stage IV lung cancer patients. Conclusions Prolonged mechanical ventilation patients had the worst long-term survival rate of all patients with chest diseases in our hospital. Successful weaning from the mechanical ventilator was most important factors for improving long-term outcomes in prolonged mechanical ventilation patients.