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Understanding the displacement of the resident wetting fluid in porous media is crucial to the remediation strategy. When pollutants or nutrients are dissolved in the surface wetting fluid and enter the unsaturated zone, the resident wetting fluid in the porous system may remain or be easily flushed out and finally arrive in the groundwater. The fate and transport of the resident wetting fluid determine the policy priorities on soil or groundwater. In this study, the displacement of the resident wetting fluid by the invading wetting fluid in porous media was simulated using direct numerical simulation (DNS). Based on the simulations of the displacements in porous media, the effect of the non-wetting fluid on the displacement was evaluated by observation and quantification, which were difficult to achieve in laboratory experiments. The result can also explain the unknown phenomenon in previous column experiments, namely that the old water is continuously released from the unsaturated porous media even after a long period of flushing with the new water. The effects of the interfacial tension, contact angle, and injection rate, which affected the immiscible fluid–fluid flow pattern, were also evaluated. Since pollutants dissolved in the wetting fluid could change the physical properties of the wetting fluid, the interfacial tensions of the resident wetting fluid and the invading wetting fluid were set separately in the simulation. Moreover, our simulation demonstrated that the consecutive drainage–imbibition cycles could improve the displacement of the resident wetting fluid in porous media. The successful simulation in this study implied that this method can be applied to predict other immiscible fluid–fluid flow in natural or industrial processes.