In this paper, a molecular dynamics simulation of three dimensional rough surface contact under different lubricated conditions was carried out. At atomic scale, mixed lubrication involves nano-asperity contact where the load is supported not only by asperities but also by a sufficient amount of confined lubricant. The contact area and pressure distribution of various lubricated conditions, e.g. dry, partially lubricated and fully lubricated, were presented. It has been found that cavities were formed between upper and lower surfaces under the load, and confined lubricant molecules were able to fill the cavity and support the load, resulting in the decrease of contact area and thus the protection of surface topography.