The 2015/2016 El Niño event reached the threshold of super El Niño event, and was comparable to the super events in 1982/1983 and 1997/1998. Interestingly, the tropical cyclones (TCs) were found to have very late onsets in the decaying years of the super El Niño events. This study discusses the causes of late TC onsets related with atmospheric circulation, disturbance sources and trigger mechanisms. The analysis shows that the western North Pacific subtropical high (WNPSH) from January-June during the decaying years of the super El Niño events were stronger than the climatic mean, which resulted in a relatively stable atmospheric state by inhibiting deep convection. As a disturbance source, the April-June intertropical convergence zone (ITCZ) during the decaying years of the super El Niño events were significantly weaker than its climatic mean. The cross-equatorial flow and monsoon trough, as important TC generation triggers, were weaker from April-June during the decaying years of the super El Niño events, which further reduced the probability of TC generation. As for the late TC onsets, the role of atmospheric circulation anomalies (i.e., subtropical-high, the ITCZ, cross-equatorial flow, and monsoon trough) were more important. The cross-equatorial flow may take as predictor of TC onsets in the decaying years of the super El Niño events.