The article presents the results of research on the influence of structural reconstructions on the hydrocarbon systems evaluation in the eastern part of the Yenisei-Khatanga trough. Based on seismic data interpretation and paleoprofiles construction, several stages of structural reconstructions in the geological evolution of the basin are established: at the Middle and Late Triassic boundary, Late Triassic and Jurassic boundary, in the Bathonian-Callovian time, Tithonian-Valanginian time, in the Barremian-Aptian time, in the Aptian-Albian time, in the Cenomanian time, and powerful reconstructions in the Cenozoic era. Based on interpretation of geochemical information of the well-core and outcrops, the characterization of the type of organic matter, the amount of initial organic carbon, the oil and gas source potential for the Late Triassic, Lower Jurassic, Middle Jurassic, Upper Jurassic, Lower Cretaceous oil and gas source rocks is given. The results of exploration of the geological structure of the region, the geochemical features of oil and gas source rocks became the basis for building a 2D basin model, which made it possible not only to identify generation kitchen, migration routes and accumulation zones of hydrocarbon fluids, but also to estimate the start time of generation and emigration of hydrocarbons, as well as the moments of interruption of these processes during periods of uplifting of the territory. Changes of the structural plan transformed the configuration of the basin, which led, on the one hand, to the formation of areas where rich in organic matter interlayers accumulated, and, on the other hand, to the interruption of hydrocarbon systems evaluation, reconfiguration and even destruction of deposits.