This paper presents a molecular dynamics simulation of the behaviours of non-polar droplets merging and also the fluid molecules interacting with a hydrophobic surface. Such behaviours and transport phenomena are popular in general micro-channel flow boiling and two-phase flow. The droplets are assumed to be composed of Lennards-Jones type molecules. Periodic boundary conditions are applied in three coordinate directions ofa 3-D system, where there exist two liquid droplets and their vapour. The two droplets merge when they come within the prescribed small distance. The merging of two droplets apart from each other at different initial distances is tested and the possible larger (or critical) non-dimensional distance, in which droplets merging can occur, is discussed. The evolution of the merging process is simulated numerically by employing the Molecular Dynamics (MD) method. For interactions with hydrophobic solid wail, a system with fluid confined between two walls is used to study the wetting phenomena of fluid and solid wail. The results are compared with those of hydrophilic wall to show the unique characteristics of hydrophobic interactions by microscopic methods.