Promoting green infrastructure (GN) as a tool for reducing natural disaster risk is promising, particularly in depopulated areas worldwide. Images of GN as being multifunctional and environment friendly seem to enhance citizens’ positive attitudes toward it. While conventional types of disaster prevention infrastructure, such as concrete levees, can completely prevent damage, GN can relieve the effects of natural hazards. By switching from conventional infrastructure to GN, societies could reduce the costs of disaster prevention infrastructure. However, the risk of disaster damage may increase in some areas. This study aimed to better understand citizens’ preference for GN. It was hypothesized that those who prefer GN are those who do not take the initiative to learn about it and that some citizens are not fully aware of the heterogeneous risks when selecting GN. To test the hypotheses, structural and measurement models, including latent variables, were developed, and structural equation modeling was performed. Data for constructing the measurement and structural equations were obtained using a web questionnaire administered by a professional research company in 2022 with 1,200 participants across Japan. Data from the portal site for the official statistics of Japan (e-Stat) were also used. The results confirm the hypothesis that individuals who favor GN are those who do not proactively seek to acquire knowledge concerning it. The findings highlight the importance of considering, in future policymaking, the possibility that citizens who prefer GN without knowledge about it may face high risks as a result of its uninformed adoption and use.