Background Oral mucositis (OM) is a common adverse effect in hematological cancer patients who have received hematopoietic stem cell transplantation (HSCT). In this study, we compared mouthwash with nystatin, aloe vera or plain water in OM prevention.Design A retrospective chart review was conducted in participants. The incidence, severity and duration of OM, duration of oral pain, and the use of antalgesics were recorded.Setting/participants Hematological cancer patients who had received HSCT from January 2014 to December 2020 in West China Hospital were included in this study.Results A total of 150 patients were included in our retrospective analysis. The nystatin group had the highest incidence (100.0%) of OM, followed by the aloe vera group (44.8%), the plain water group had the lowest incidence of OM (20.0%), and the nystatin group had the highest severity and the longest duration of oral mucositis. The incidence, severity and duration of pain in the nystatin group were significantly higher than the aloe vera group and plain water group, and the use of analgesic drugs in the nystatin group was also significantly higher than the other two groups (P<0.05).Conclusions In our hospital setting, plain water mouthwash achieves great effect in OM prevention in hematological cancer patients who have received HSCT.