This paper demonstrates the effectiveness and superiority of Empirical Mode Decomposition (EMD) in projecting non-stationary hydrological data. The study focuses on daily Sea Surface Temperature (SST) sequences in the Niño 3.4 region and uses EMD to forecast the probability of El Niño events. Applying the Mann–Kendall test at the 5% significance level reveals a significant increasing trend in SST changes in this region, particularly noticeable after 1980. This trend is associated with the occurrence of El Niño and La Niña events, which have a recurrence interval of approximately 8.4 years and persist for over a year. The modified Oceanic Niño Index (ONI) proposed in this study demonstrates high forecast accuracy, with 97.56% accuracy for El Niño and 89.80% for La Niña events. Additionally, the EMD of SST data results in 13 Intrinsic Mode Functions (IMFs) and a residual component. The oscillation period increases with each IMF level, with IMF7 exhibiting the largest amplitude, fluctuating between ±1 °C. The residual component shows a significant upward trend, with an average annual increase of 0.0107 °C. These findings reveal that the EMD-based data generation method overcomes the limitations of traditional hydrological models in managing non-stationary sequences, representing a notable advancement in data-driven hydrological time series modeling. Practically, the EMD-based 5-year moving process can generate daily sea temperature sequences for the coming year in this region, offering valuable insights for assessing El Niño probabilities and facilitating annual updates.