Because of limited resources, each year during the period from 1999 through 2007, only about one-quarter of the 111 counties in Guangxi province were selected by means of risk assessment to participate in Supplementary Immunization Activities (SIAs), targeting children aged 8 months to 14 years during 1999-2003 and 8 months to 10 years during 2004-2007. Approximately 2 million doses of measles vaccines were administrated each year during SIAs. Estimated from the National Notifiable Diseases Surveillance System, with a reliable internal consistency over years, the average annual incidences of measles before SIAs (1993-1998), during the first phase (1999-2003), and during the second phase (2004-2007) were 16.05, 9.10, and 2.46 cases per 100,000, respectively. The overall provincewide annual incidence decreased by 84.67%, from 12.12 cases per 100,000 in 2000 to 2.10 cases per 100,000 in 2007. The percentage of counties with annual incidence ≥10 cases per 100,000 decreased from 55% in 1993 to <1% in 2007. Compared with the pre-SIA period, the greatest decrease in annual incidence was 83.93% for the 10-14.9-year-old group and the smallest decrease was 46.16% for children <1 year old. The multiple-year SIAs targeting children in selected high-risk counties were effective in controlling measles in mountainous, impoverished, and multiethnic measles-endemic areas.