The aim of study was to explore the better detection method for cytomegalovirus (CMV) in allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients and to compare the efficiency of fluorogenic quantitative PCR (FQ-PCR), flow cytometry (FCM) and ELISA. The plasma DNA loading and serum level of IgM antibody against CMV in 214 clinical specimens from 19 allo-HSCT patients were detected by real-time FQ-PCR and ELISA respectively, the pp65 antigen in 118 peripheral blood leukocyte samples were measured by FCM. The results showed that the positive rates of pp65 antigen, IgM antibody and DNA load were 30.85% (58/188), 13.08% (28/214) and 35.51% (76/214) respectively, the coincidence between their sequential detection positive rates and clinical diagnosis were 7/8, 7/8 and 3/8 respectively. There was no statistical significant difference between the positive rate of pp65 antigen and of DNA amount (P > 0.05), and they have manifested relationships (P < 0.05). The positive rate of IgM antibody detected by ELISA was obvious lower than that of DNA quantitated by FQ-PCR and pp65 antigen detected by FCM, but the difference between them showed statistical significance (P < 0.05), Smaller relativity was found between IgM antibody detection and the other two methods (P > 0.05). It is concluded that FQ-PCR and FCM are sensitive, rapid, suitable and reliable methods for monitoring recipient reactive CMV infection of allo-HSCT recipients and are worthy to extensively use for guiding antiviral therapy.