The Zaisan Basin is a unique geological structure that preserves a most complete sedimentary archive of late Mesozoic through most of the Cenozoic era. A century of studies brought very rich data on the stratigraphy and geological history of the Zaisan sedimentary sequence. The recent scientific progress made it possible to refine the Cenozoic stratigraphic scale of the region. Here we present the results of a detailed morphostructural analysis and propose morphotectonic zoning of the Zaisan Basin based on the modern tectonic and geodynamic concepts. New results of magnetostratigraphic dissection of the Kalmakpai stratotypic section, the most complete section of the sedimentary strata of the depression, and its comparison with the drilling data of its axial part are presented. By the synthesis of magnetostratigraphy with the rich regional biostratigraphic record we refine the stratigraphy of the region and clarify dynamics of tectonic movements and the development of relief and landscapes of the Zaisan Depression and the bounding alpine structures of Saur-Tarbagatai during the Cenozoic.