Background: Staphylococcus aureus (S. aureus), particularly methicillin-resistant Staphylococcus aureus (MRSA), remains the predominant cause of infections in drug users. The cross-sectional study aims to elucidate the prevalence, risk factors, phenotypic and molecular characteristics of S. aureus carriage among community-based drug users.Methods: All eligible drug users, both intravenous and oral drug users, were asked to complete questionnaires and collect nasal swabs during the period between May and December 2017 in Guangzhou, China. Swabs were processed for identification of S. aureus. Antimicrobial susceptibility test and polymerase chain reaction assays were used to detect phenotypic and molecular characteristics for identified isolates. Univariate and multivariate logistic regression analyses were used to assess risk factors for S. aureus carriage.Results: Overall, 353 drug users were included in the study and the prevalence of S. aureus carriage was 15.01% (53/353). The prevalence of MRSA carriage was 6.80% (24/353). Cohabitation was a risk factor for S. aureus (adjusted OR=8.80, 95% CI: 1.89-40.99). The proportion of multidrug resistance was 54.72% for S. aureus isolates and most of these isolates were resistant to penicillin, erythromycin and clindamycin. Seventeen MRSA isolates were multidrug resistant. The results of clonal complexes (CCs) and sequence types (STs) for S. aureus were diverse. The three predominant types for CCs were CC5 (64.15%, 34/53), CC59 (11.32%, 6/53), and CC7 (7.55%, 4/53); and for STs were ST188 (20.75%, 11/53), ST5 (11.32%, 6/53), and ST59 (11.32%, 6/53). Conclusion: The prevalence of S. aureus nasal carriage was lower when the prevalence of MRSA carriage was moderate. Phenotypic and molecular characteristics of S. aureus isolates, particularly MRSA isolates, revealed serious antibiotic resistance, indicating the existence of cross-circulation, and implying high opportunity of virulence-related diseases. Decolonization might be considered for drug users with MRSA carriage.