Under health pattern in new era，functional food will display unique charm and definitely play an important role in promoting the health of people. Based on the survey data from Beijing and Shanghai，the paper take kids’ functional yogurt as subject and use the choice experiment to research consumer preference and willingness to pay for the attributes of different functional material，organic certification and the country of origin in kids’ yogurt. The results indicate that consumers pay the most attention to origin，secondly organic certification，and finally functional material；Consumers are willing to pay additional 5.384 Yuan，5.384 Yuan，3.893 Yuan，3.563 Yuan and 2.411 Yuan for children yogurt made in New Zealand，the yogurt with organic certification，the yogurt added vitamin，probiotic and calcium，respectively. The factors that education，consumption frequency，income and cognition affect consumers’ preference and willingness to pay for different attributes of children yogurt. Therefore，this paper puts forward the countermeasures and suggestions to promote the development of kids’ functional food in China.