Condom use is often equated to safer sex. The prevalence of condom use during sex work among female sex workers (FSW) in China is high. Condom use, however, co-exists with condom failure and improper use and hence risk of HIV transmission. In a cross-sectional study, we interviewed 195 FSW in Shenzhen, China. The prevalence of condom use in the last episode of sex work was 97.4 %, However, respectively 53.8 and 86.2 % had experienced at least one condition of condom failure that may lead to genital contact (wearing condoms after penetration, condom breakage/slippage, condoms removed by clients) and at least one condition of improper condom use (not removing air from the tip of the condom, not pulling it down to the root of penis and not choosing good quality condoms). Factors of individual level (e.g. never choosing high quality condoms for sex work), inter-personal level (e.g. agreement to have unprotected sex if fond of clients or paid more) and environmental/structural level (e.g. non-availability of condoms) were associated with various types of condom failure and improper use. Although HIV prevention interventions have increased prevalence of condom use among FSW, the risk of HIV transmission may still be high as “unsafe” sex due to condom failure and improper use is prevalent. Interventions promoting safer sex need to address such issues and take socio-ecological factors into account. Condom use during sex work is not equivalent to well protected sex as the protective effects could be compromised by frequent condom failure and improper use.