Thick successions of middle and late Cenozoic sedimentary rocks occur in the Linxia Basin of China. These deposits comprise an archive recording spatiotemporal patterns of mountain uplift, erosion, basin deformation, and associated changes in the monsoon, as a result of the growth of the northeastern Tibetan Plateau. The Linxia Basin is also world famous for its abundant and diverse vertebrate fossils that shed light on Cenozoic terrestrial ecosystem evolution; however, previous studies of these important fossils have been beset by issues related to commercial excavation and associated difficulties in ascertaining provenance, with many specimens in private collections. Despite years of intensive studies by geologists from Lanzhou University and vertebrate paleontologists from the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), aspects of basin stratigraphy and chronology still remain controversial. The heart of these controversies often revolves around questions of imprecise fossil provenance and related casual references of fossils as age tie-points, different interpretations of lithostratigraphic units at different localities across the basin, and ultimately different age determinations. In this special issue, entitled Biostratigraphy, Chronostratigraphy and Vertebrate Paleontology of the Linxia Basin, we report the findings of an IVPP project, funded by the Chinese Academy of Sciences, which addresses these controversies, proposes a new age model for basin, and develops understanding of the fossil assemblages. In this introduction to the special issue, we review the tectonic context for basin evolution and chronology as well as lithostratigraphy, paleoenvironments and climates. While issues of provenance remain challenging and will continue to burden Chinese vertebrate paleontologists into the future, our findings shed new light on the vertebrate paleontology of the Linxia Basin, and unique circumstances in which it developed. •Linxia Basin in Gansu Province produces rich Cenozoic vertebrate fossils.•Basin sediments reflect tectonic evolution of northeastern Tibetan Plateau.•Basin structure and surrounding mountains influenced paleoclimate.•Fossils and sediments are useful for paleoenvironmental interpretations.•We highlight controversies over chronologic interpretations of strata and fossils.