Background: Vitamin A deficiency is recognized as a major public-health nutrition issue in the developing countries. Limited hospital sources and sample sizes are available in most of the existing studies associated with healthy school-age children. The aim of this study was to compare vitamin A status of 6- to 13-year-old healthy children in China between 2002 and 2012. Methods: According to China National Nutrition and Health Survey 2002 (CHNNS2002) and CHNNS2010-2013, we choose 6- to 13-year-old children as the research object. We measure the serum retinol concentrations of the children using high performance liquid chromatography (HPLC). The children were divided into two groups: 6- to 9-year-old and 10- to 13-year-old. The areas were divided into urban and rural area. Results: Total number of the children (6- to 13-year old) was 8170 in 2002 survey, and it was 6016 in 2012 survey. In 2012, the vitamin A level of the children was higher than that in 2002 (t = 39.26, p = 0.000). The level of vitamin A in 10- to 13-year-old group was higher than that in 6- to 9-year-old group across areas and genders between 2002 and 2012. There was no difference on the incidence of vitamin A deficiency in all the children between 2002 and 2012, but in 2012 the incidence of vitamin A deficiency in the urban children was higher than that in 2002 (x(2) = 45.456, p = 0.000). The incidence of vitamin A deficiency in 10- to 13-year-old group was lower than that in 10- to 13-year-old group across areas and genders between 2002 and 2012. In 2012, the incidence of marginal vitamin A deficiency in the children was lower than that in 2002 (x(2) = 861.604, p = 0.000). Similar phenomena were also found in across area groups. The incidence of marginal vitamin A deficiency in 10- to 13-year-old group was lower than that in 6- to 9-year-old group across areas and genders between 2002 and 2012. There was no difference in vitamin A status of the children across the area, gender and age groups between 2002 and 2012. Conclusion: Vitamin A nutritional status of the children in 2012 has been significantly improved compared with that in 2002. However, vitamin A deficiency was still a moderate public health problem in Chinese children, especially in younger school-age children. Consequently, controlling the incidence of vitamin a deficiency is imperative for promoting Chinese children's health.