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This dataset contains underlying data and results of 3D gas hydrate modelling at the southern Hikurangi Margin using PetroMod™ software and accompanies a manuscript published in the Geochemistry Geophysics Geosystems journal (DOI10.1029/2019GC008275). The model integrates thermal and microbial gas generation, migration and hydrate formation. Modelling these processes has improved the understanding of factors controlling hydrate distribution. Three spatial trends of concentrated hydrate occurrence are predicted. The first trend (I) is aligned with the principal deformation front in the overriding Australian plate. Concentrated hydrate deposits are predicted at or near the apexes of anticlines and to be mainly sourced from focussed migration and recycling of microbial gas generated beneath the hydrate stability zone. A second predicted trend (II) is related to deformation in the subducting Pacific plate associated with former Mesozoic subduction beneath Gondwana and the modern Pacific-Australian plate boundary. This trend is enhanced by increased advection of thermogenic gas through permeable layers in the subducting plate and focussed migration into the Neogene basin fill above Cretaceous‒Paleogene structures. The third trend (III) follows the northern margin of the Hikurangi Channel and is related to the presence of buried strata of the Hikurangi Channel system.