The industrial innovative development of the fuel-energy complex of the Republic of Kazakhstan contributes to the increase of the economic effect of the complex oil refining with the accompanying release of valuable components and elimination of harmful emissions into the environment at extracting and processing of hydrocarbon raw materials. In the given case the economic effect can be expressed through the cost of the output products received at the processing of hydrocarbon raw materials taking into account quality parameters and fractional composition of Kazakh oil. The received calculation data on the deposits in Buzachi show that the potential value of each ton of the refined oil in this area is 3-4 times higher than the selling prices of 1 ton of the crude oil, and on average reach the value of 251.85 dollars (Karazhanbas oil, for example) against 70-79 dollars per ton. It is noteworthy that a high percentage of the profit gained from oil refining (circa 89%) is related to the release of high-viscosity (viscosity index of 55-85 and more) distillate base oil and precious metals (vanadium and nickel pentoxide), and in particular, in Karazhanbas oil. It will be economically justified owing to the sale of metals at high price in the world market (for example, 1 kg of vanadium pentoxide of 97% purity costs around 25 dollars). In Tengiz oil a high percentage of the profit gained from oil refining (the potential value of products received for oil refining equals 263.06 dollars) accounts for individual hydrocarbons – circa 85%, fuel fractions – 10%, condensed gas - 3.5%. Thus, special attention should be paid to modern technologies applied in oil refining and the increase of the output of fuel fractions. Based on the analysis of harmful emissions into the environment - pentoxide of vanadium and nickel, formaldehydes, ammonia, and the rate of losses (circa 33 million 336 thousand dollars per year) in the national economy at exploitation of oil and gas deposits, the following conclusion can be drawn: many useful components (such as vanadium and others) that exist in Kazakh oil and are concentrated in crude oil, heavy oil residues and the production wastes are the main sources of the environmental pollution. The rate of the damage caused by the emission of these metals into the environment accounts circa 91% in the deposit of Buzachi (in comparison with other harmful emissions). Moreover, formaldehydes and ammonia, sulfur compounds and sulfur (71% in Tengiz deposit in the gross share of emissions) that have not been further used in manufacturing and are openly stored in the premises of oil refining enterprises are the dominating factors causing contamination of water reservoirs near Tengiz oil deposit. The manuscript is aimed at preparing Master students and PhD students of technical and economic specialities, as well as at scientific staff, engineers and technicians dealing with the issue of introduction of the innovations in subsoil use and complex use of mineral resources.