BACKGROUND Obesity is widespread in the world including developing countries. However malnutrition in poor areas is still a serious problem. Few investigations, especially in a large sample, have been performed in Western area of China. This study aimed to evaluate the nutritional status of school children aged 9-15 years in large Southwest city of China, and identify the differential impact of aberrant birth categories and family history of obesity related disease on childhood overweight and obesity development. METHODS A multistage random cluster sampling was performed to evaluate the prevalence of thinness, overweight and obesity, which were defined by the new age-, sex-, specific BMI reference developed by World Health Organization (WHO) (2007). And then a frequency matched case-control study was performed to identify the risk factors of overweight and obesity. RESULTS 7,194 children (3,494 boys, 3,700 girls) were recruited, and 1,282 (17.8%) had excess bodyweight (14.5% overweight, 3.3% obesity). The combined prevalence gradually decreased with age, and were more prevalent among boys than girls (P <0.05). Meanwhile 6.3% were found thinness and there were little differences in genders (P >0.05). Preterm large for gestational age (OR = 2.746), maternal history of obesity related disease (OR = 1.713), paternal history of obesity related disease (OR = 1.583), preterm appropriate for gestational age (OR = 1.564), full term small for gestational age (OR = 1.454) and full term large for gestational age (OR = 1.418) were recognized as significant risk factors in the multivariate regression analysis (P <0.05). CONCLUSIONS While overweight and obesity was dramatically spreading, malnutrition still remained a serious problem. This unmatched nutritional status should be emphasized in backward cities of China. Children born of both preterm and LGA, whose parents particularly mothers had a history of obesity related disease, should be emphatically intervened as early as possible.