Declining total fertility rates pose a severe challenge to the economy, society, culture, and politics of any region. Low fertility rates among China’s rural floating population with strong fertility are aggravating these challenges. Previous research has confirmed the relationships between health insurance and fertility intention. However, it is still unclear whether the existing association is favorable or not. Moreover, the majority of existing studies in China employ data from either urban or rural populations, whereas evidence from rural floating populations remains scarce. Based on the “China Migrants Dynamic Survey (CMDS)” in 2016, the current study used the logistic regression model to explore the impact of health insurance policy on the fertility intention of the rural floating population in China. Propensity Score Matching (PSM) was used to address potential selection bias. Three important findings were observed: Firstly, participating in the Basic Medical Insurance System (BMISUR) significantly improved rural floating populations’ fertility intentions in China. Secondly, the association between age and the fertility intention of the floating population was “inverted u-shaped” with the highest fertility intention among those aged 25 to 34. There was also a positive correlation between personal income and fertility intention, and it was found between local housing purchase, formal employment, the co-residents scale, and the fertility intention in the rural floating population in China. Interprovincial mobility was positively associated with the fertility intention among rural migrants. Thirdly, the impact of health insurance policies on the fertility intention of the rural migrant population varies by gender, age, and inflow areas. The aforementioned findings can guide the Chinese government in its efforts to improve the fertility intention of the rural floating population, reform the social security system with a focus on “targets”, and implement differentiated welfare policies aimed at promoting the equalization of basic public services, thereby contributing to China’s population structure and long-term development.