Objective To investigate optional therapeutic strategies for suspected Pneumocystsis carinii pneumonia (PCP) and/or cytomegalovirus (CMV) pneumonia by microbial screening and control experiment. Methods Microbial screening included 3 parts, which were microbiological microscopy for patients’ lung specimens and bronchoalveolar lavage fluid (BALF), detection of serum CMV antibody by ELISA and detection of serum CMV DNA content by fluorescence quantitative PCR. The patients who were positive to only CMV or PCP were respectively divided into 2 groups, that is, the combined treatment group and the single treatment group (CMV or PCP as corresponded). The length of hospital stay and the remission rate after 14 days'treatment were compared between the 2 groups. Results There were totally 136 positive patients, including 17 only positive to CMV, 21 only to PCP and 98 with double positive of PCP and CMV. The length of hospital stay were shorter in the combined treatment group than the single treatment groups (W=162.5, P=0.006). The remission rate were also obviously higher in the former than the latter groups (χ2=6.454, P=0.011). Conclusion It is quite common for mixed infection of PCP and CMV pneumonia, but rare for single infection. So, the combined treatments are more effective than the single one.