As one of the important driving forces of sustainable development in coastal areas, foreign direct investment (FDI) has provided new ideas for exploring optimal strategies. This analysis explores the linear impact of FDI on sustainable development in coastal areas with 53 cities in China from 2012 to 2020. Accordingly, a dynamic panel smoothed transition regression (PSTR) model is used to analyze the non-linear impact of FDI on sustainable development, with transition mechanisms of industrial structure and technological innovation level. The findings reveal that the non-linear effect of FDI on the sustainable development of coastal areas is obvious. When the coastal area’s industrial structure is more optimized, and the level of technological innovation is higher, the promotion effect of FDI on sustainable development is more obvious. Further, the threshold effect of industrial structure and technological innovation is different. The threshold conversion rate of industrial structure is faster, but the threshold effect of technological innovation is stronger. Regionally, the impact of FDI on the sustainable development of coastal adjacent areas is significant, but not on the sustainable development of inland areas due to the few FDI inflows. This analysis offers guidance for policymakers to further develop the tertiary industry, increase financial investment in innovation in coastal areas and encourage enterprises to improve their independent innovation capacity.