Post-transplant cyclophosphamide (PTCy) treatment has been increasingly used in allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, its effects on the burden and severity of oral mucositis (OM) remain unclear. A total of 177 patients received allo-HSCT with PTCy treatment at Xiangya Hospital between 2015 and 2020. Among them, 140 patients whose OM was prospectively graded using the World Health Organization (WHO) oral toxicity scale were included in this retrospective study. The grafts were peripheral stem cells from matched (28/140, 20.0%) and mismatched (112/140, 80.0%) donors. Conditioning intensity was categorized as myeloablative conditioning (MAC; 82/140, 58.6%) or reduced intensity conditioning (RIC; 58/140, 41.4%). The overall incidence of any OM was high (116/140, 82.9%) but the incidence of severe OM was relatively low (40/140, 28.6%). The median duration of OM was 10 days (2–22 days post-transplantation) from day –2 to day +15 (median day +8). Earlier onset of OM was correlated with greater severity. Multivariate analysis showed that conditioning intensity (MAC vs RIC, odds ratio [OR] 6.128, 95% confidence interval [CI] 2.319–16.198) and donor type (mismatched vs matched, OR 3.252, 95% CI 1.089–9.717) were associated with increased risk of severe OM. No significant implications of severe OM were observed on acute or chronic GVHD. Patients with severe OM had slightly worse overall survival, but the difference was not statistically significant (p = 0.078). Therefore, severe OM does not appear to lead to a worse transplant outcome if an intensified oral care protocol is adopted.