Human leukocyte antigen (HLA) partially matched related donor (PMRD) hematopoietic stem cell transplantation (HSCT) is an effective option for hematological malignancies. In this study, the nonmalignant late effects of PMRD HSCT were evaluated and compared with HLA-identical sibling donor (ISD) HSCT. Three hundred thirteen patients (ISD, n = 160; PMRD, n = 153) who survived at least 6 months and received regular follow-up examinations after their HSCT were enrolled. The 5-year cumulative incidence (±SE) of at least one late effect and multiple late effects was 47.30% ± .17% versus 58.21% ± .16% (P = .134) and 17.97% ± .10% versus 34.28% ± .15% (P = .001) for PMRD HSCT recipients versus ISD HSCT recipients, respectively. The cumulative incidence of keratoconjunctivitis sicca, periodontitis, ankylosis, myalgia, and nephrotic syndrome was lower among PMRD HSCT recipients compared with ISD HSCT recipients. Severe chronic graft-versus-host disease, multiple pre-HSCT chemotherapy cycles, female donor, and older age were risk factors for at least one late effect. Female donor, older age, and long-term immunosuppressive therapy were associated with multiple late effects. In summary, PMRD HSCT recipients have a lower risk of late effects compared with ISD HSCT recipients, possibly due to differences in protocols for graft-versus-host disease prophylaxis, and long-term follow-up after transplantation is recommended.