Considering that there is not a systematic evaluation method for prime farmland selection and assignation, an evaluation index system was built up including soil quality, grain production, land use status and regional economic level. Aiming at food security, prime farmland protection target of Jiangsu Province was assigned to each county based on a combinatorial evaluation method. The results showed that social and economic factors weighted much more than soil quality and grain production in the assignation. With rapid urbanization and industrialization, most of the counties in Jiangsu Province had reached a precipice of farmland lost and desiderated a transformation of development model to an intensive one. The research would contribute to prime farmland planning in the new run of the land use comprehensive planning.