This study aimed to provide reference for evaluating the achievability of hepatitis B virus (HBV) elimination in a high endemicity city with universal neonatal vaccination in place for over 30 years. Between September 2018 and October 2020, 2085 citizens from 1143 geographically random households in Hong Kong completed a questionnaire and had blood-testing for HBV markers (anti-HBs, HBsAg, anti-HBc, HBeAg). We evaluated the epidemiology and examined factors associated with HBV exposure, vaccination and chronic diseases. The proportion of households with HBsAg positive index participants was 9.2% (95% CI 7.5%–10.9%). The age- and sex-adjusted HBsAg prevalence was 6.3% (95% CI 5.3%–7.4%), compared to >10% in those born in 1960-1970 and among non-local born citizens, and <1% in people born after introduction of neonatal vaccination. Among 155 HBsAg positive participants, 59% were aware of their infection status with 10% on treatment and 10/150 (6.7%) HBeAg positive. More than 40% (872/2064) tested negative for both HBsAg and anti-HBs, contributed by the lack of immunity in older adults and the waning immunity of vaccines. Hong Kong has remained at high-intermediate HBV endemicity state. The moderate level of anti-HBs positivity and very low treatment coverage (10%) among HBsAg positive participants pose challenges for achieving the HBV elimination target.