This is a study of the storm surge trends in some of the typhoon-prone coastal areas of China. An unstructured-grid, storm surge-wave-tide coupled model was established for the coastal areas of Zhejiang, Fujian and Guangdong provinces. The coupled model has a high resolution in coastal areas, and the simulated results compared well with the in situ observations and satellite altimeter data. The typhoon-induced storm surges along the coast of the study areas were simulated based on the established coupled model for the past 20 years (1997–2016). The simulated results were used to analyze the trends of the storm surges in the study area. The extreme storm surge trends along the central coast of Fujian Province reached up to 0.06 m/y, significant at the 90% confidence level. The duration of the storm surges greater than 1.0 and 0.7 m had an increasing trend along the coastal area of northern Fujian Province, significant at confidence levels of 70%–91%. The simulated trends of the extreme storm surges were also validated by observations from two tide gauge stations. Further studies show that the correlation coefficient (R_TE) between the duration of the storm surge greater than 1 m and the annual ENSO index can reach as high as 0.62, significant at the 99% confidence level. This occurred in a location where the storm surge trend was not significant. For the areas with significant increasing storm surge trends, R_TE was small and not significant. This study identified the storm surge trends for the full complex coastline of the study area. These results are useful both for coastal management by the government and for coastal engineering design.