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.