The main methods of calculating the composition of geochemical systems in the thermodynamic equilibrium state were considered in the article. It was shown that the basis for such calculations was the determination of the Gibbs Free Energy of each system components at given temperatures and pressures. The methods of Gibbs Free Energy calculation at standard pressure and under conditions that are realized within the sedimentary strata were analyzed. The equations of state for natural gas individual components were selected and their Gibbs Free Energies for heat fluxes ranging from 40 to 100 mW/m2 and depths of 0–20 km were calculated. The results showed that the pressure significantly affects the value of Gibbs Free Energies formation of natural gas components within the sedimentary strata. Changes of the Gibbs Free Energies of natural gas components formation, as a function of depth, subordinated to the same laws for each compound. This regularity was better expressed in more heated areas. It was shown that with depth increasing the Gibbs Free Energy of natural gas components formation first rapidly decreases and reaches its minimum ranging from 2 to 6 km. Moreover, as the value of the heat flux increases, the maximum value of the Gibbs Free Energy of formation of natural gas components, expressed in kilometers, decreases. With further immersion/deepening to depths greater than 6 km, the Gibbs Free Energy of the formation of natural gas components gradually increases, and in areas with greater heat flux, a sharp increase was characteristic, and with less, it was slow and weakly expressed. There is a stability area for hydrocarbon and non-hydrocarbon components of natural gas ranging from 2 to 6 km. With the increase of Carbon number in the hydrocarbon chain, the value of Gibbs Free Energy of the natural gas hydrocarbon components formation decreases, which indicates the presence of a stability zone for heavy natural gas components (it should be expected that oil also) within the depths of 2–6 km.