Understanding the interfacial heat transfer and thermal resistance at an interface between two dissimilar materials is of great importance in nanoscale systems. The experimental study of interfacial heat transfer in nanoscale systems is complex due to the difficulty of fabricating and handling these objects at length scales below ≈10 nm. These challenges can be overcome by using computational tools, such as classical molecular dynamics (MD) simulation techniques, which allows the modelling of molecular structure and its interactions at atomic length and time scales precisely. This work introduces a new and reliable linear response method for calculating the interfacial thermal resistance or Kapitza resistance in fluid-solid interfaces with the use of equilibrium molecular dynamics (EMD) simulations. MD simulations are carried out in a Lennard-Jones (L-J) system with fluid confined between two solid slabs. Different types of interfaces are tested by varying the fluid-solid interactions (wetting coefficient) at the interface. It is observed that the Kapitza length decreases monotonically with an increasing wetting coefficient, as expected. The theory is further validated by simulating under different conditions such as channel width, density, and temperature. The predicted Kapitza length shows an excellent agreement with the results obtained from both EMD and non-equilibrium MD simulations. Furthermore, this method will be used to predict the Kapitza resistance for confined fluids under flow conditions, particularly for superhydrophobic systems such as water in graphene channels and carbon nanotubes, where frictional forces are minimal and so too energy dissipation. For such systems, both velocity and temperature profiles are almost flat, making NEMD measurements of slip and Kapitza lengths very difficult.