VanB phenotype-vanA genotype vancomycin-resistant Enterococcus faecium (VREF) has never been reported in mainland China. We investigated the frequency and molecular characteristics of this strain in a Beijing tertiary hospital. Of 23 vanA genotype VREF clinical isolates, 12 (54.3%) were VanB phenotype-vanA genotype. Mutilocus sequence typing (MLST) analysis revealed that all isolates belong to a single clonal complex (CC78), which has been disseminated worldwide. Based on MLST and pulsed-field gel electrophoresis, 23 isolates were polyclonal dissemination in our hospital. Tn1546-like element structure analysis showed that of 12 VanB phenotype-vanA genotype isolates, 5 had complete deletion of vanY and vanZ accompanying insertion of IS1216V in vanX-vanY intergenic region, 5 had ISEfa4 insertion in orf2-vanR intergenic region, a new Tn1546 structure type, and 2 were identical to VanA phenotype-vanA genotype VREF. Data showed that the deletion of vanY and vanZ genes or ISEfa4 insertion in orf2-vanR intergenic region can partly explain the causes of difference between phenotype and genotype.