The aim of this study was to characterize vancomycin-resistant Enterococcus faecium (VREfm) isolates phenotypically and molecularly, and investigate associations between the virulence factors enterococcal surface protein (esp), hyaluronidase (hyl), and collagen adhesin (acm) and colonization/infection. A total of 126 E. faecium [66 VREfm and 60 vancomycin-susceptible (VSEfm)] were collected in West China Hospital. Nine E. faecium isolates (7 VREfm and 2 VSEfm) were selected at random for comparative study in a large region from China. Minimum inhibitory concentrations (MICs) were measured by Etest and agar dilution, vancomycin resistance genes (vanA, vanB, and vanC) and virulence genes (esp, acm, and hyl) were detected by polymerase chain reaction (PCR). Thirty-four VREfm underwent repetitive sequence-based PCR (rep-PCR) and multi-locus sequence typing (MLST). One linezolid-resistant isolate (MIC = 8 μg/ml) was found; none were tigecycline resistant. All 73 VREfm (28 infective strains and 45 intestinal colonizers) had the vanA gene and VanA phenotype. Positivity for esp, hyl, and acm in VREfm was 79.5, 46.6, and 86.3%, respectively, which was higher than in VSEfm (54.8, 27.4, and 56.5%, respectively). Among VSEfm, positivity for acm in isolates from pleural or cerebrospinal fluid (84.6%) was higher than that from blood (32.4%). There were 11 rep-PCR types (similarity >95%) and MLST revealed nine sequence types (STs) among the selected isolates. Most VREfm and all VSEfm belonged to clonal complex 17. A new ST was found, with allele sequence (15, 1, 38, 1, 1, 1, 1). In China, most VREfm seem to belong to the classical nosocomial CC17 clone, and many of them have acquired virulence genes, further strengthening a hospital-adapted type.