Understanding time-changing tidal characteristics is essential for numerous practical purposes, such as flood prevention, navigation, and ocean engineering. Previous studies mainly focus on tidal evolution in coastal areas while tidal changes in deep water areas receive limited attention due to the lack of long-term high-frequency sea level records. In this paper, we extract the inter-annual and decadal tidal variability in the South China Sea (SCS) from 24 coastal tide gauges and 25-year satellite altimeter observations using the novel S_TIDE toolbox. Through numerous sensitivity experiments, it is found that ~17 independent points (IPs) are suitable for extracting inter-annual and decadal tidal variability in the deep basin of the SCS. It is also found that tidal variability and sea level variability are closely correlated in most parts of the SCS. The high correlation between tidal variability and sea level variability in the central deep basin of the SCS is associated with the El Niño–Southern Oscillation(ENSO). The results obtained from satellite data are less stable and accurate than those obtained from long-term tidal gauge observations, but the methods described here provide a strong foundation for future research on time-varying tidal dynamics using the combination of tide gauges and satellite altimeter data.