Many residents from the rural areas gain urban hukou status and become the new permanent urban migrants because China has been implementing the hukou system （the household registration system） and has been in the period of the rapid urbanization. It is of significant policy value to analyze the health risks of the nongzhuanfei group （the permanent migrants from rural areas）. The objective of this paper is to identify the differences in perceived health risks between the urban natives and the nongzhuanfei group based on the panel data of China Health and Retirement Longitudinal Study in 2013 and 2015 and the method of sample selection corrections. The results indicate that: firstly, the effects of education and hukou on the health risks of urban migrants from rural areas are much underestimated without sample selection corrections; secondly, the nongzhuanfei group has achieved upward mobility, however, compared to the urban natives, they have significantly higher perceived health risks whether in middle-aged or elderly periods; thirdly, compared to the urban natives, the nongzhuanfei group with low and middle education degree has significantly higher perceived health risks, however, there are no significant differences between the nongzhuanfei group and the urban natives with advanced education; fourthly, higher education can effectively reduce health risks of both the urban natives and the nongzhuanfei group; fifthly, compared to the urban natives, the nongzhuanfei group has higher possibility to be ill during the past month. The placebo and robust tests show that the results are still reliable. Based on the previous literature, this paper explores the mechanism that the nongzhuanfei group has higher health risks. They experience more serious malnutrition and could not enjoy the same quality and quantity education and healthcare as the urban natives when they lived in the rural areas. Even at present, the children in rural China are confronted with many risks, such as malnutrition, poor accessibility to public health services and low enrollment rate of senior schools. Therefore, more attention should be paid to the health risks of the new nongzhuanfei group with low and middle education during hukou system reform and urbanization. The governments can take some measures to reduce health risks of the new nongzhuanfei group, such as carrying out universal sensor school education and the higher enrollment rate of college, disseminating health knowledge and advocating health behaviors.