During the Miocene, major global cooling occurred during two intervals: the middle Miocene (∼14–13 Ma) and the late Miocene (∼7‐6 Ma). The Antarctic Ice Sheet expanded substantially at ∼14–13 Ma, and glaciation in the Northern Hemisphere was initiated at ∼7–6 Ma. Although the causes of these two global cooling events remain unclear, paleoclimate modeling provides an important approach for investigating the mechanisms. However, paleoclimate modeling relies on paleogeographic boundary conditions, and many uncertainties remain regarding the land–sea distribution, topography, and bathymetry of the Miocene; specifically, previous published paleogeographic reconstructions for the middle and late Miocene show several discrepancies with each other. Here, we present two new sets of global topographic and bathymetric boundary conditions for the middle Miocene (∼14 Ma) and late Miocene (∼6 Ma). Our new reconstructions use a published plate kinematics model, oceanic lithospheric paleo‐ages, and oceanic sediment thicknesses and incorporate global fossil records, stratigraphy, lithofacies, paleoenvironment, and paleoelevation data. With these data, we further constrain the conditions of several important intercontinental and marginal seas surrounding Eurasia and the Arctic, the depth of major seaways in tropical latitudes and middle‐high latitudes of the Northern Hemisphere, and global paleotopography, especially that of the Tibetan Plateau and the Andes.