In deep oil reservoirs, the existence of associated gas generally has a crucial impact on crude oil properties and flow performance. In this work, adopting molecular dynamic simulation, we studied the occurrence characteristics of oil with associate gas methane (the molar ratio of methane to oil rm/o were 1/4, 2/3, 3/2, and 4/1) in nano-pore throat and the displacement behavior of oil and methane in the water flooding process. Simulation results indicated: (1) an increasing replacement of the adsorption-status oil by methane as the methane content increased; (2) the oil and methane displacement efficiency was enhanced as the methane content increased in the water displacement oil and gas process; (3) the threshold displacement pressure gradually decreases as the methane content increases. The microscopic characteristics of the occurrence features and displacement performance of crude oil with associated methane in nano-pore throat were discussed in detail, and the underlying mechanism was discussed at the length concerning the interaction between different components. Our work provides an in-depth understanding of the occurrence characteristics and flow resistance of oil with associated gas in deep oil reservoirs.