The Pearl River Delta region (PRD) is one of the regions seriously threatened by sea level rise and storm surges in Chinese coastal area in the context of global climate change, which causes huge loss of farmland and agricultural production. Based on the relevant research and experience, a loss evaluation model of farmland yield caused by sea level rise and storm surge was established. In this model, the submerged farmland area, cropland area and per unit yield of each kind of crops were concerned, while the impact of wind, flood time, changes of land use and plant structure were not considered during the long prediction term. Taking the PRD in Guangdong as the study area, this paper estimated and analyzed spatial distribution and losses of farmland in different scenarios in the years of 2030, 2050 and 2100, using the digital elevation model, land-use data, the local crop structure, rotation pattern, and yield loss ratio at different submerged heights obtained by field questionnaire investigation. The results showed that the proportion of submerged farmland and losses of agriculture production in the PRD would increase gradually from 2030 to 2100. Yangjiang, Foshan and Dongguan were the areas where submerged farmland increased obviously, while Guangzhou and Zhuhai were the areas with slow increase of submerged farmland. Besides, with sea level rising, the submerged farmland with higher submerged height increased, while that with lower submerged height declined. As for agricultural production, vegetables would have the greatest loss than rice and peanuts. From the point of cities, it was Jiangmen that had the greatest loss of rice. Shanwei and Jiangmen were the areas with serious loss of vegetables. Although the losses of peanut were generally smaller, Jiangmen, Guangzhou and Shanwei had the relatively high losses. At last, some suggestions were put forward, such as building sea wall and tidy gate in Jiangmen, Huizhou and Shanwei, enforcing ecological protection to mitigate storm surges and strengthening disaster warning.