Objective To explore clinical characteristics of human cytomegalovirus (HCMV) and polyomavirus (BKV and JCV) infection after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Methods Clinical data of 53 patients with hematologic malignancies who underwent allo-HSCT from June 2016 to December 2017 were collected. HCMV, BKV and JCV loads in patients' peripheral blood and urine were monitored once a week from day 1 to day 100 after transplantation. Incidence, occurrence time, clinical manifestations, and risk factors of viral infection were analyzed. Results A total of 51 patients had viral infection, infection rate was 96.23%. HCMV, BKV, and JCV infection rates were 54.72% (29/53), 77.36% (41/53), and 28.30% (15/53) respectively. Incidences of pulmonary infection, acute graft-versus-host disease (aGVHD), and hemorrhagic cystitis (HC) were 54.72%, 58.49%, and 20.75% respectively. Analysis on risk factors showed that aGVHD (OR, 24.61[95% CI, 2.30-46.24]), pretreatment with total body irradiation (TBI) (OR, 33.39[95% CI, 1.57-79.13]), and use of antithymocyte globulin (ATG) (OR, 24.77[95% CI, 1.16-52.58]) were independent risk factors affecting HCMV. Human leukocyte antigen (HLA) coincidence (OR, 0.003[95% CI, 0.00-0.10]) could reduce the risk of HCMV viruria; pretreatment with TBI (OR, 15.10[95% CI, 1.14-39.27]) was an independent risk factor for BKV viruria, compatible blood group of donor and recipient (OR, 0.07[95% CI, 0.01-0.64]) could reduce the risk of BKV viruria. Conclusion HCMV and polyomavirus infection in blood and urine of recipient should be monitored as soon as possible after transplantation, so as to prevent and reduce complications in time.