PurposeAccording to the Christensen stochastic roughness model, the purpose of this study is to developing a modified Reynolds equation to investigate the effects of surface roughness and molecular rarefaction on ultra‐thin compressible and isothermal gas lubrication.Design/methodology/approachBasing upon the average film thickness method with three adjustable coefficients, the higher order slip‐flow velocity distribution was accommodated.FindingsCompared to the smooth case, the longitudinal roughness improves the pressure distribution and load carrying capacity, while the effect of transverse roughness is opposite to that of longitudinal one. The molecular rarefaction effect may diminish the built‐up air bearing pressure and reduce the roughness effect on load carrying capacity. The squeeze number has evident effect in depression of maximum pressure of slider rail with transverse roughness.Originality/valueCombing the high‐order slip‐flow model and Christensen roughness model, this research paper proposed a feasible study of the analysis of molecular rarefaction effect on slider air‐bearing system.