In this article, typomorphic associations of microelements in carbonaceous caustobioliths and oils are defined as indicators of naphthogenesis based on the analytical survey of the literature and our own research. Various approaches to the studying of crude oil genesis from the position of abiotic and complex approaches (polygenesis) are considered. Such approaches are relevant to the prospect and development of offshore oil deposits, localized at ultra-deep levels. For deep deposits, the most prominent hypothesis of oil origin is the abiogenious theory. In the foundation of that approach lays the assumption that hydrocarbons are formed mainly due to reactions of the formed mantle gases and the host rock. Key factors for these reactions to proceed are specific conditions concerning temperature, pressure, and specific catalysts. The article presents the results of thermodynamic and quantum-chemical modeling of the possibility of the organic and organometallic compound formation using the software package HSC Chemistry 6.0. Pointed out the possibility of a low molecular weight hydrocarbon formation due to the contact of ascending flows of mantle gases with cooling natural barriers. The primary synthesis proceeds with the interaction of fluid forms of H2, CO2, and H2S. The estimation of the bonding energy depending on the structure of organometallic compounds was performed using the Avogadro software package. The program used the method of bond potential energy minimization to find the most stable structure of molecules. The metals nickel and vanadium, as the main companion metals of oil, are of the most interest from the position of analysis of their form of existence in the possible formation of hydrocarbons. Vanadium’s and nickel’s accumulation in asphaltene fractions of oils, probably, is caused by complex compounds of metalloporphyrin’s formation. In addition, the high sulfur content is probably associated with polymerization of organic molecules due to the formation of di-sulphide bonds. The method of cavitation extraction of organometallic compounds from oil and complex mineral−oil raw materials has been developed for experimental confirmation of microelements the extraction capability from oil raw materials.