Transportation is the backbone of developing regional economies and the evolution of our civilization. Well planned road systems are essential to connect dispersed communities or cities. However, roads are one of the major destructive forces to regional ecosystems and the natural environment. The effects of roads on their adjacent ecosystems may include road kills, habitat fragmentation, barrier effect to animal movement, road edge effects, introduction of exotic species, pollution and noise, change of micro-climate, etc. This study undertakes a comprehensive survey of road kills in Kinmen (Taiwan) and analyzes their causes. The road crossing behaviors of animals have been utilized in deriving survival probability by employing Traffic Flow Theory. Two models, Traffic Flow Model and Linear Model, have been proposed in this study and comparisons of survey results and the models are also carried out. Comparing the survey results and predictions of models, both models yield similar results for moderate traffic flow and provide excellent agreement in predicting frequency of road kill of birds and small mammals. It is found that traffic volume, adjacent landscape and road condition are the major factors in road kills. Higher traffic volume near animals’ habitats always augments the probability of road kill, however roadside trees, adjacent landscapes, and road longitudinal slope may also affect the probability of successful crossing by small animals, especially birds. The barrier effect of roadside trees forces birds to fly between tree trunks and enter onto a collision course with oncoming vehicles, so that dense roadside trees may lead to higher bird casualties. On the other hand, roads with abrupt turns or steep longitudinal slopes may block the view of small animals and may be a significant factor in increasing the probability of being run over by vehicles. Based upon the findings of this study, some mitigation measures to lower road kill probability are