We have developed a three-dimensional polymer density functional theory (DFT) and applied it to predict the thermodynamic and structural information of molecular transport through a surfactant-covered interface. The green recursive function method has been employed to consider the chain conformation effect. The reference ideal gas method has been developed, extending it from molecular DFT to polymer DFT, with a universal form to calculate thermodynamic properties such as the grand potential and free energy. We have demonstrated the accuracy of the theory by comparing it to available simulations. Furthermore, we have applied the theory to predict the free energy barrier and density profile of molecular transport through a surfactant-covered interface. The free energy profile provides reasonable predictions of the transition velocity, while the density profile gives insight into the microstructural information of the transport process, which is consistent with the available molecular simulations. (c) 2017 American Institute of Chemical Engineers AIChE J, 63: 238-249, 2018