The Pearl River Delta on China’s coast is a region that is seriously threatened by sea level rise and storm surges induced by global climate change, which causes flooding of large areas of farmland and huge agricultural losses. Based on relevant research and experience, a loss evaluation model of farmland yield caused by sea level rise and storm surges was established. In this model, the area of submerged farmland, area of crops, and per unit yield of every type of crop were considered, but the impact of wind, flooding time, changes in land use and plant structure were not considered for long-term prediction. Taking the Pearl River Delta region in Guangdong as the study area, we estimated and analyzed the spatial distribution and loss of farmlands for different scenarios in the years 2030, 2050, and 2100, using a digital elevation model, land-use data, local crop structure, rotation patterns, and yield loss ratios for different submerged heights obtained from field survey and questionnaires. The results show that the proportion of submerged farmlands and losses of agricultural production in the Pearl River Delta region will increase gradually from 2030 to 2100. Yangjiang, Foshan, and Dongguan show obvious increases in submerged farmlands, while Guangzhou and Zhuhai show slow increases. In agricultural losses, vegetables would sustain the largest loss of production, followed by rice and peanuts. The greatest loss of rice crops would occur in Jiangmen, and the loss of vegetable crops would be high in Shanwei and Jiangmen. Although losses of peanut crops are generally lower, Jiangmen, Guangzhou, and Shanwei would experience relatively high losses. Finally, some measures to defend against storm surges are suggested, such as building sea walls and gates in Jiangmen, Huizhou, and Shanwei, enforcing ecological protection to reduce destruction from storm surges, and strengthening disaster warning systems.