Allogeneic hematopoietic stem cell transplantation (HSCT) is an effective therapy for patients with hematologic malignancies. Severe pneumonia is associated with high mortality rate in HSCT recipients. Viral co-infection indicates a poor prognosis of HSCT recipients. In this study, a total of 68 allogeneic HSCT recipients were included. Cytomegalovirus (CMV) and Respiratory syncytial virus (RSV) infection was assessed by testing peripheral blood and oropharynx swabs, respectively, collected in the first 180 days after transplantation. We analysed the correlation of CMV and RSV co-infection with severe pneumonia and mortality. The incidence of CMV and RSV co-infection was 26.5% (18/68). Severe pneumonia was diagnosed in 61% (11/18) cases with co-infection compared to only 10% (5/50) cases with mono-infection or no infection. The analysis of potential risk factors for severe pneumonia showed that CMV and RSV co-infection was significantly associated with severe pneumonia (p < 0.001). The 5 patients who died of severe pneumonia were all co-infected with CMV and RSV. In conclusion, CMV and RSV co-infection appears to be an important factor and facilitates the development of severe pneumonia in allogeneic HSCT patients with hematologic malignancies.