Infrastructure development has caused extensive habitat fragmentation, and increased traffic raises the number of wildlife roadkills. Wildlife crossing structures (WCSs) can prevent roadkills and protect wildlife. Amphibians commonly comprise the highest proportion of roadkills. Nevertheless, adequate WCSs suitable for amphibian crossing and migration are lacking. This study aimed to suggest a design proposal for a WCS for amphibians based on a behavioral experiment. First, we evaluated the home range, protection value, and roadkill trends of Bufo gargarizans, Bombina orientalis, and Rana uenoi. We selected six factors that can affect anuran migration preferences: noise level, tunnel width, light-shielding level, construction material, tunnel substrate, and tunnel shape. Each species selected a migration path, and mobility was confirmed in different structures. The animals’ preferences were evaluated by counting the number of migrating individuals in each migration experiment. Overall, the three species showed a preference for 60 dB of noise and a tunnel width of D700 (mm). Migration frequencies were higher at 35% light-shielding level and when the substrate was soil. PVC was the preferred construction material for tunnels, and mobility was the highest in circular tunnels. We proposed a design for WCSs that incorporated the preferences of these three target species.