Currently, the purchase of medical insurance for the migrant population in China is mostly voluntary. As a result, the rate of their medical insurance participation has been relatively low and there exists a great internal disparity. The influential factors involving government, society and migrants themselves are all likely to have an impact on their actual participation in medical insurance.. Previous studies have yielded different and often conflicting conclusions about the specific effects of these factors. In order to find the truth and clarify the differences, the present study, based on the 2011-2012 National Monitoring Data of the Migrant Population, conducted a comparatively meticulous analysis of the factors influencing the medical insurance participation of migrants by means of descriptive statistics, cross-over analysis, logistic model analysis and multi-level analysis. The results are as follows: (1) The overall rate of medical insurance participation of the migrant population is about 69% while the rate of urban medical insurance participation is about 26%. (2) Overall, the rate of medical insurance participation for migrants is not high enough, and there is a large internal differentiation with an obvious Matthew Effect. Among them, especially those with low education or low income laid-off workers, people having no fixed jobs, housewives and migrant children, or those engaged in catering, housekeeping, domestic decoration, agriculture, forestry, animal husbandry, fishery and irrigation, have an obviously low rate of medical insurance. (3) The rate of insurance participation is significantly related with gender, age, marital status and other demographic characteristics, but their impacts are diverse. (4) The rate of participation is also significantly related with migrants’ family size, migration experience, willingness to settle down and their host provinces. (5) The migrants’ social participation and integration has a significant positive effect on their joining medical insurance, especially urban medical insurance with higher benefit. (6) The greater the proportion of migrant population in a community, the greater disparity in the rate of urban medical insurance participation among different genders, marital statuses, employment statuses and industries, and the smaller disparity among different occupations. (7) The quality of service and assistance provided by the community has a double effect on relations between the rate of medical insurance participation and the contributing factors. That is to say, the higher the quality, the stronger the correlation between the rate of urban medical insurance participation and the migrants’ education and their household registration type, and the smaller the difference among different employment statuses. Based on these findings, we argue that the rate of insurance participation should be examined from the community perspective as well as the individual perspective. Accordingly, several suggestions are proposed to improve the rate. (1) The service and assistance from community should go to migrants with special difficulties, especially those with low education or low income, and those unemployed or engaged in farming, construction, catering and retail. (2) The communities concerned should launch humanized propaganda and organize information activities related to medical insurance, especially communities with more migrants than residents, villages–in-city, communities in suburban areas, communities of small enterprise clusters and construction sites. (3) Improve and reform the content and methods of community service so as to attract migrants to participate in the self-management and self-service of the community. (4) Reform the blueprint of medical insurance system to increase the coverage of migrants’ unemployed family members; probe into the occupation-biased medical insurance policy to protect the medical insurance right for the most vulnerable migrants; and gradually balance the benefit rates among different types of medical insurance and eventually integrate all kinds of medical insurance at the national level.