In 2014, the South Korean government initiated the “Nutria Eradication Project” to actively manage and control populations of nutria, an invasive alien species that threatens national biodiversity. In the present study, we examined domestic nutria habitats in 2014 to 2018 and analyzed spatial shifts in habitat distribution to develop management policies and eradication strategies for the South Korean Ministry of Environment. A total of 27,487 nutria individuals were captured over five years upon the initiation of the eradication project. We found that the number of habitat tracks decreased from 1510 in 19 administrative districts in 2014 to 176 in 14 districts in 2018. We examined the distribution of nutria habitat tracks and found a northwestward shift at an average angle of 313.9° and 46,656.9 m. This distribution shift prompted improvements in control policies focused on nutria capture to suppress rodent movement and shifting distributions. We redefined the spatial scope of our control regions accordingly and established isolated environments in each region to prevent further spread. Additionally, resource management was focused in areas showing habitat expansion. Overall, we observed an estimated 54% decrease in nutria habitat tracks from 2016 to 2017. Our results have since been enacted in government policies and provide a basis for establishing flexible strategies for effectively controlling nutria habitats and populations. In 2017, the South Korean government allocated additional funds for research and for the development of further control strategies working toward the project’s goals.