Intestinal worm infection adversely impacted child health and was one of the China's largest health burdens. However, yet little was known about associations between intestinal worm infection and malnutrition in school-aged children in rural China. This study aimed to fill into the gap.Data were from a survey of children aged 9-11 years old in Guizhou Province, China conducted in June 2013. Considering anemia and low intelligent quotient (IQ) as mediating factors, binomial logistic regression was used to estimate the associations of intestinal worm infection with thinness, underweight, and stunting. Moreover, the associations between socio-demographic factors and malnutrition were also explored.Among 2179 children, part of children was infected by intestinal worm (41.85%). Stunting (28%), low memory IQ (87.52%), and low process IQ (62.59%) were highly prevalent in the sample. Socio-demographic factors were associated with thinness, underweight, stunting, low memory IQ, low process IQ, anaemia, and intestinal worm infection. Intestinal worm infection was associated with low IQ, anemia, and stunting. In addition, anemia and low IQ could not confound the other expected associations.This study demonstrated the association between intestinal worm infections and stunting appeared to be largely mediated via low IQ. The study highlighted the importance of deworming and improving nutrition in the surveyed areas.