Objective To investigate the incidence of central line-associated bloodstream infection (CLABSI) in patients with hematopoietic stem cell transplantation (HSCT), explore risk factors for the occurrence of CLABSI. Methods Basic information of patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) who underwent HSCT in a hematology department from November 1, 2016 to October 31, 2017 was collected, incidences of original CLABSI (OCLABSI) and modified CLABSI (MCLABSI) were calculated, related risk factors were analyzed by multivariate Cox regression. Results A total of 218 patients with AML and MDS who underwent HSCT were enrolled, 19 of whom had OCLABSI and 10 had MCLABSI. Twenty-one strains of pathogens were isolated from 19 patients with OCLABSI, including 9 gram-positive bacteria, 11 gram-negative bacteria, 1 fungus; 9 strains were multidrug-resistant organisms. The main risk factors for OCLABSI included the female (HR=0.088;95%CI:0.017-0.440;P=0.003), age (HR=1.560;95%CI:1.066-2.530;P=0.034), bone marrow cell transplantation only (HR=4.408;95%CI:1.860-22.593;P=0.043), ATG/CSA/MMF/MTXG for preventing graft-versus-host disease (GVHD) (HR=0.101;95%CI:0.015-0.686;P=0.019), and MTX for preventing GVHD (HR=0.097;95%CI:0.011-0.816;P=0.032). Conclusion Definition of MCLABSI can provide more accurate monitoring on deep central venous catheter-related bloodstream infection. Incidence of CLABSI in HSCT patients can be reduced by early detection of high-risk population according to high-risk factors, strict adherence to the prevention and control measures of bloodstream infection, and implementation of immune recombination after enhanced transplantation.