Occupational allergic respiratory disease in healthcare workers due to occupational exposure has received widespread attention. At the same time, evidence of altered respiratory flora associated with the development of allergy has been found in relevant epidemiologic studies. It is of concern that the composition of nasopharyngeal flora in healthcare workers differs significantly from that of non-healthcare workers due to occupational factors, with a particularly high prevalence of carriage of pathogenic and drug-resistant bacteria. Recent studies have found that interventions with upper respiratory tract probiotics can significantly reduce the incidence of respiratory allergies and infections. We searched PubMed and other databases to describe the burden of allergic respiratory disease and altered respiratory flora in healthcare workers in this narrative review, and we summarize the mechanisms and current state of clinical research on the use of flora interventions to ameliorate respiratory allergy, with the aim of providing a new direction for protecting the respiratory health of healthcare workers.