Changes in agricultural yields due to climate change will affect land use, agricultural production volume, and food prices as well as macroeconomic indicators, such as GDP which is important as it enables one to compare the climate change impacts across multiple sectors. This study considered five key uncertainty factors and estimated macroeconomic impacts due to crop yield changes using a novel integrated assessment framework. The five factors are 1) land-use change (or yield aggregation method based on spatially-explicit information), 2) the amplitude of the CO2 fertilization effect, 3) the use of different climate models, 4) socioeconomic assumptions and 5) the level of mitigation stringency. We found that their global impacts on the macroeconomic indicator value were 0.02 - 0.06% of GDP in 2100. However, the impacts on the agricultural sector varied greatly by socioeconomic assumption. The relative contributions of these factors to the total uncertainty in the projected macroeconomic indicator value were greater in a pessimistic world scenario characterized by a large population increase and low income (0.6%) than in an optimistic scenario (0.00%).