Objective To understand the growth and health care status of children under five years old in project counties of Chongqing and Sichuan, so as to provide evidence for establishing scientific and effective measures for health care of children. Methods The non-probability sampling method was used to select the children under five years old from 54 villages in 6 project counties in Chongqing and Sichuan. The parents were investigated by questionnaire; the height (length) and weight of children were examined; and the hemoglobin of 6-35 months old children was determined. Multivariable logistic regression analysis was conducted to examine the factors influencing the growth status of children under five years old. Results Totally 1 089 caretakers of children under five years old were investigated; 82.1% (894/1 089)of them had an educational background of primary school or middle school; and the median net per capita income of their family was 2 500 yuan (RMB) in 2009. For the youngest children in the families, the hospital delivery rate was 86.6% (933/1 077), the colostrums feeding rate was 96.4%(1 050/1 089), and the average of weaning months was (11.6±5.6) months. The prevalence of diarrhea of the children was 19.6%(213/1 089) within the past two weeks, and 264 children had cough (24.2%). A total of 1 197 children under five years old were investigated, the rates of stunting, underweight and wasting were 17.4%(200/1 152), 4.7%(55/1 173)and 2.2%(25/1 148), respectively. The underweight rate of boys was significantly higher than that of girls(5.9%\[38/645\] vs 3.2%\[17/528\]; χ2=4.638,P=0.031), and the wasting rate of boys was also significantly higher than that of girls(3.0%\[19/634\] vs 1.2%\[6/514\]; χ2=4.460,P=0.035).The detection rate of low hemoglobin among the 6-35 months old children was 38.4%(272/709). Multiple variable logistic regression analysis showed that male sex, born at home, and low birth weight might be the influence factors on the low growth status of children under five years old. Conclusion The caretakers of children under five years old in rural areas of Chongqing and Sichuan have a low cognitive level on the health care of children, and the children have developmental delay and malnutrition to various extents. Measures should be taken to improve child health care knowledge and health education.