Changes in climate mean state profoundly impact climate variability. Here, we quantify slow changes in the mean climate induced by the variations in the Earth’s orbit from mid- to late Holocene, and their feedback on the main modes of climate variability. We focus on the Indo-Pacific system and show that mid-Holocene conditions favored the dominance of an equatorial dipole mode in the Indian Ocean (IO), independent of the El Niño Southern Oscillation (ENSO) and different from the IO Dipole (IOD) observed today. Mean state changes induced a gradual shift to an IO basin mode that along with the IOD modulates most of the IO variance at present. The climate modes evolution and their connectivity changes are investigated over 6,000 years using a complex network methodology and principal component analysis. To characterize the nature of this transition, we explore the trajectory of the Indo-Pacific climate by accounting for its spatiotemporal and multivariable dependency. The full trajectory of the system is explored from a dynamical system perspective by constructing a state space representation. The manifold embedded in the 104 -dimensional state space provides a compact representation of the system evolution and points to a gradual shift of the basin of attractions in the tropics. This approach, together with a mean state analysis, reveals that a strengthening of the Walker circulation set the stage for a shift in modes in both basins.