Objective To compare of status of malnutrition between premature/low birth weight infants(PLBW) and normal term infants(NT),in order to analyze factors causing infants malnutrition. Methods Two sample counties were random selected from the ones that satisfied the research conditions in Shaanxi province and Chongqing of western China.472 PLBW and 461 NT aged 6 to 36 months from the two counties were investigated from September 2010 to November 2010.The SPSS 19.0 and MlwiN 2.25 software were applied to analyze data using general statistical analysis and multilevel regression model. Results The prevalence of malnutrition in PLBW and NT were 22.0% and 10.0%(P<0.01) respectively,among this,stunting were 18.4% and 8.9%(P<0.01) respectively,underweight were 4.9% and 3.0%(P>0.05) respectively,wasting were 2.8% and 1.1% (P>0.05) respectively.The results of multilevel regression suggested that PLBW(OR=1.612),older age(OR=1.207),disqualification of feeding index(OR=3.089),partial eclipse(OR=2.077) and anemia(OR=2.001) were risk factors to lead malnutrition of infants. Conclusion The prevalence of malnutrition of PLBW is higher than that of NT,especially on stunting in western rural China and impropriate feeding practices of supporters are main influencing factors to lead malnutrition.