Background: Child mortality can be reduced by 20% with the caregivers’ appropriate health seeking behaviors. Therefore, in order to reduce child mortality in remote areas, we examined the Health Seeking Behavior (HSB) of caregivers of sick children under five years old in Moyu County, Southern Xinjiang, which is the remotest and poorest areas in China, and the factors influencing HSB of caregivers.Methods: We analyzed the factors influencing the health seeking behavior of 846 caregivers of sick children with a questionnaire survey in Chinese and Uighur by a cross-sectional study. Binary logistic regression analysis was used to predict the influencing factors on HSB of caregivers. Results: After the children’s illness was detected, 89.94% caregivers took their children to go to the doctor. 44.91% caregivers took their children to the doctor in the public medical institutions, while 40.07% caregivers chosen the private medical institutions. Compared with the private medical institutions, public medical institutions were likely to be chosen when caregivers consider the treatment cost or the children with cough, runny nose and stuffy nose, but considering children’s age (0.5times), reputation of doctor (0.6times), adequate drug resources (0.5times), the traditional habits on HSB (0.5times), and time to get to hospital (0.2times), the public medical institutions weren’t be chosen.Conclusions: The HSB of the caregivers for sick children in Southern Xinjiang isn’t optimistic. The doctors’ competencies, the quantity of medicines, the distance, the traditional habits influencing caregivers to choose hospitals, which is also the most significant thing to promote the health of rural children in Xinjiang and northwest China.