Background During our clinical practice, some patients with Chlamydia psittaci pneumonia were found to have secondary pulmonary fungal infections; consequently, this study analyzed the risk factors for their combined pulmonary fungal infections. We also compared the efficacy of tetracycline and moxifloxacin in the treatment of C. psittaci pneumonia to guide the treatment of this disease.Methods Eighty cases of C. psittaci pneumonia in Chongqing were selected and divided into a non-fungal group (56 cases) and a fungal group (24 cases) according to the combination of pulmonary fungal infection. The risk factors for combined pulmonary fungal infection were analyzed. According to the type of medication used, the patients were divided into five treatment groups, including (I) 12 cases of omadacycline, (II) 12 cases of tigecycline, (III) 10 cases of doxycycline, (IV) 8 cases of minocycline, and (V) 38 cases of moxifloxacin, and the efficacy of the drugs was compared.Results (1) Comparisons of factors, including hospitalization cost, length of stay, and duration of fever, showed that, first, the prognosis of the non-fungal group was better than that of the fungal group, and second, there were statistically significant differences between the two groups in the use of broad-spectrum antibacterial drugs; the co-administration of antimicrobials; combined structural lung disease, diabetes mellitus, and liver disease; and serum ferritin levels at admission. A logistic regression analysis showed the co-administration of antimicrobials; combined structural lung disease, diabetes mellitus, and liver disease; and relatively low serum ferritin were independent risk factors for combined pulmonary fungal infections. (2) Comparison of drug efficacy: The white blood cell count in Group I was better than in groups II and V, while fever, imaging improvement, and calcitoninogen decrease time in Group I were significantly better than in groups II, III, IV, and V. The cost in Group V was lower than in groups I, II, and III, and no significant difference was seen in the occurrence of major adverse reactions.Conclusions Patients with C. psittaci pneumonia who are co-administered with antimicrobials and are combined with structural lung disease, diabetes mellitus, and liver disease along with relatively low serum ferritin need to be alerted to combined pulmonary fungal infections. The efficacy of tetracyclines in treating such infections is more pronounced than that of other drugs, while the cost of moxifloxacin is lower than that of other antibiotics.