Current perspectives on lower frequency variations and secular warming have predominantly been shaped by traditional anomalies that assume an annual cycle (AC) with a time-invariant amplitude. However, this anomaly framework falls short in capturing the complexity of multiple periodic modes with intricate waveforms and time dependent amplitude—the traits, in general, shared by externally forced responses of complex dynamical systems. By allowing interannual amplitude modulation of ACs, we show that the monotonic amplitude increases of the first AC of Sea Surface Temperature (SST) are manifested as the basin-wide secular warming of the ocean surface. Notably, the first SST-AC exhibits significant interannual variances and the largest linear warming rates in the Pacific Warm Pool. While the linear warming pattern mirrors that of a long-term mean SST, it depicts an entirely different warming pattern on the surface of the tropical Pacific Ocean compared to those reported so far. Moreover, all interannual warm (El Niño) and cold (La Niña) events in tropical Pacific regions are abnormal interannual modulations in the third and fourth ACs of SST, respectively. Specifically, a strong El Niño event occurs when a positive amplitude modulation leads to the overlap of two consecutive positive phases of the third AC of SST. Conversely, the absence of such overlaps during negative amplitude modulations significantly contributes to the positive skewness of SST anomalies. No systematic decadal changes in the zonal propagation characteristics of SST in the eastern Pacific (EP) and central Pacific (CP) regions were detected. These findings underscore that the secular warming and low-frequency events in EP and CP are intrinsic to three distinct ACs.