The introduction of science-intensive technologies that ensure a high level of energy content and restoration of ecological balance in places of extraction and processing of commercial resources is the main condition for the successful development of independent Kazakhstan. This paper concentrates on challenges of studying the mechanisms of chemical effects on oil-reservoir rocks functioning in order to increase oil recovery. Relevance of addressing the challenges is determined by necessity to increase profitability of fossil hydrocarbons mining. The article is prepared based on the results of the works carried out within the framework of the Program of the State Science Academies for 2013-2020 period. “Earth Sciences” geological library Section No.9, “Integrated discovery and conservation of the Earth subsoils” line of fundamental research # 132, innovative processes of mineral deposits development and advenced processing of mineral raw materials”, “The Fundamental Basis of Oil and Gas Industry Innovative Technologies” project, No.ААА - 0139-2018- 0006.