In order to optimize the recovery and long-distance transportation technology of the emerging energy resource, natural hydrogen, the complex thermodynamic properties of the natural hydrogen production mixture is focused in this paper, aiming at improving the development, purification and pipeline transportation operation of natural hydrogen based on the multi-component phase equilibrium analysis. Commencing with the second law of thermodynamics and following the criteria of of reducing the total energy and increasing the total entropy in a system, a thermodynamic-consistent flash calculation method is formulated by using the Onsager reciprocal relations to construct a time-dependent evolution scheme of mole composition and volume over time. The dissipative nature of the algorithm's energy behavior is substantiated. Based on this iterative flash calculation method, a thermodynamics-