The rapid rural urban migration and aging has generated an over-depopulation problems in rural areas since the 1980s. The purpose of this study constructs the marginal size of rural over-depopulated village through the analysis of the residential disparities such as farmer’s ratio, basic life service accessibility, and levels of social and economic factors for each village community. This marginal scale could support evaluating diverse rural policies, which have been planned to apply to the rural development programs at the village level. The major challenges for over-depopulated villages are the lack of basic facilities, production infrastructures and inactive communities in the village. Therefore, the quantitative analysis of rural residential disparities according to rural village scale can provide the criteria for rural over-depopulated villages. We utilized Korea Agricultural Survey Data(2010) including specific residential condition of village level. The present study adopt multinomial-logit model for quantitative analysis of different village scales and decomposition techniques to separate the direct effect by the village scale factor from the endowment effects by regional or area characteristics, and residual effect by unknown factors. The present study found that the minimum scale of a rural over-depopulated village was 40 and 60 houses for the respective conditions of farmer’s ratios less than 50% and greater than 75%. It was concluded based on the study findings that threshold scale could support evaluating the diverse rural policies, which have been planned to apply to the rural development programs at the village level.