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Mechanical systems on all length scales may be subjected to nanoscale thin film lubrication (TFL). Molecular dynamics (MD) simulations were conducted to investigate the lubrication mechanism and boundary slip of squalane confined in nanogap at 293 K with two different film thicknesses and a wide range of pressures. The molecular distribution, density and velocity profiles of squalane were analyzed. The results show that the lubricant atoms tend to form layers parallel to the wall, but the lubricant molecules orient randomly throughout the film in the directions both parallel and perpendicular to the wall. Most squalane molecules appear twisted and folded, and extend to several atomic layers so that there are no slips between lubricant layers. The distances between the lubricant layers are irregular rather than broadening far away from the walls. The boundary slip at the interface of bcc Fe (001) and squalane only occurs at high pressure because of the strong nonbond interactions between lubricant atoms and wall atoms. The tendency of boundary slip is more obvious for films with thinner film thickness. According to the simulations, the relationship between the slip length and the pressure is given.