Amid the ever-increasing urgency to develop oil fields with complex mining and geological conditions and low-efficiency reservoirs, in the process of structurally complex reservoir exploitation a number of problems arise, which are associated with the impact of layer fractures on filtration processes, significant heterogeneity of the structure, variability of stress-strain states of the rock mass, etc. Hence an important task in production engineering of such fields is a comprehensive accounting of their complex geology. In order to solve such problems, the authors suggest a methodological approach, which provides for a more reliable forecast of changes in reservoir pressure when constructing a geological and hydrodynamic model of a multi-layer field. Another relevant issue in the forecasting of performance parameters is accounting of rock compressibility and its impact on absolute permeability, which is the main factor defining the law of fluid filtration in the productive layer. The paper contains analysis of complex geology of a multi-layer formation at the Alpha field, results of compression test for 178 standard core samples, obtained dependencies between compressibility factor and porosity of each layer. By means of multiple regression, dependencies between permeability and a range of parameters (porosity, density, calcite and dolomite content, compressibility) were obtained, which allowed to take into account the impact of secondary processes on the formation of absolute permeability. At the final stage, efficiency of the proposed methodological approach for construction of a geological and hydrodynamic model of an oil field was assessed. An enhancement in the quality of well-by-well adaptation of main performance parameters, as well as an improvement in predictive ability of the adjusted model, was identified.