There has been an ongoing debate on the strengthening of the GM food labeling system in Korea. In order to effectively assess the impacts of strengthening GMO labeling policy from the production side, the fundamental research on the rise of the expected cost in food production is needed. In this study, the input ratio of GM raw material costs within production costs, which are variable costs in the production of food, is analyzed by classifying the GM raw material cost for food products into 22 categories. Scenario analysis is carried out to make reasonable assumptions on how much GM soybeans and corn is demanded by food manufacturing companies that are sensitive to the acceptability of GM food by domestic consumers. Three scenarios are designed in such a way that the input ratio of GM raw material cost is assumed to be 100%, 75%, and 50%. As a result of scenario analysis, the food product with the highest GM input ratio in the final goods is found to be edible oils (28.2%), and the input ratios of GM for tofu or jellied food, soy milk, and paste are relatively low at 2.4%, 1.7%, and 3.4%, respectively. The results of this analysis suggest that if GM raw materials are replaced with non-GM raw materials, the effect of cost increase will be concentrated on the food products with a high GM raw materials input ratio.