The Manihiki Plateau is a Large Igneous Province (LIP) located in the western Pacific. It has been proposed that the Manihiki Plateau was emplaced as a part of the “Super-LIP” Ontong Java Nui by multiple magmatic phases during the Cretaceous Normal Superchron. The break-up of the “Super-LIP” caused the fragmentation of the Manihiki Plateau into three sub – provinces, which all exhibit individual relicts of the LIP break-up. We examined two deep crustal seismic refraction/wide-angle reflection profiles crossing the two largest sub-plateaus of the Manihiki Plateau, the Western Plateaus and the High Plateau. The modeling of P- and S-wave velocities reveals astonishing differences in the crustal structure between the two sub-plateaus. Whereas the High Plateau shows a constant crustal thickness of 20 km, relicts of multiple volcanic phases and break-up features at its margins, the models of the Western Plateaus reveal a Moho depth decreasing from 17 to 9 km. There is only little evidence of secondary phases of volcanic activity. Therefore, the main morphological structures on the Western Plateaus are fault systems and sedimentary basins. These significant differences in the crustal structure infer, that the initial break-up of the “Super-LIP” can be further constrained by the tectonic and magmatic activity exposed on the Manihiki Plateau. We therefore postulate that the initial break-up was characterized by rifting between the Hikurangi and the Manihiki Plateau with little crustal stretching, while massive crustal stretching occurred in the area of the break-up towards the Ontong Java Plateau along with rotational forces. These findings contribute to a better understanding of the plate-tectonic framework of the Pacific Ocean during the Cretaceous Normal Superchron, and the role of Large Igneous Provinces in this plate circuit.