The research of tidal changes is vital to ocean engineering, the protection of flooding as well as the utilization of ocean resources in coastal areas. Previous studies are mainly based on long-term hourly tide gauges whose number and location are highly limited. Previous study indicated that the long-term trends of tidal amplitudes are abnormally large in the central deep basin of the South China Sea (SCS) based on 25-year satellite altimeter data, which is not realistic and the resultant of the interference of ocean mesoscale variability on tidal harmonic analysis. In this paper, we use 27-year T/P-Jason satellite altimeter data processed by X-TRACK software to study the long-term tidal trends in the SCS. The satellite altimeter data processed by X-TRACK obviously improves the accuracy and completeness of satellite data in the SCS. Meanwhile, the weighted least square method is used to eliminate the effect of tidal aliasing caused by long period sampling. We find that in most areas of the SCS, the amplitudes of four major tidal constituents have significant long-term trends. The significant positive and negative long-term trends of amplitudes and phases are mainly distributed in the coastal areas such as the western Luzon Strait, the Strait of Malacca and Taiwan Strait, where the water depth and shoreline change dramatically. The largest positive long-term trend of amplitudes can reach 2.75 mm/a and the largest negative long-term trend of amplitudes can reach −2.16 mm/a. The long-term trends of tidal amplitudes in the SCS should be related to river flow and human interference.