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Both El Nino-Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) are important indicators of the potential impact of climate at the global scale. The IOD-ENSO relationship at different timescales is temporally non-uniform, which is important to understand in order to evaluate its socioeconomic impacts. Here, we developed and applied a wavelet cross-correlation analysis approach for investigating the evolution of the IOD-ENSO relationship over a 150-year period. We found that the IOD-ENSO relationship was statistically significant at the dominant timescales of 1.5, 3, and 24year, with the correlation degree varying with time. The hysteresis effect between IOD and ENSO and the evolution of their relationship obviously differ at the three dominant timescales. The positive (negative) IOD and El Nino (La Nina) events were mainly determined by the variability of IOD and ENSO at the timescale <3year. Strong positive IOD events in the September-October-November period would more likely be related to El Nino events 2months later and La Nina events 14months later, but negative IOD events would rarely co-occur with El Nino or La Nina events. The result achieved in this study can serve as a useful guide for the long-term forecast of IOD and ENSO.