To analyze the effects of non-Newtonian lubricants and surface roughness in journal bearing lubrication, a modified Reynolds equation is derived. In the equation, differential viscosity and the first normal stress function are defined to specify the rheological properties of non-Newtonian medium. Flow factors are used to specify the effect of surface roughness. The modified Reynolds equation is numerically calculated using super over relaxation method. Numerical results of the lubrication show that the differential viscosity is the principal non-Newtonian property affecting the lubrication, it is determined by the material parameters of the lubricant and is affected by the shearing rate. Under its effect, the load capacity of non-Newtonian lubricants is not always higher or lower than that of Newtonian lubricants'. The effect of the first normal stress difference increases under the conditions of dynamic loading. Surface roughness shows an obvious effect on load capacity when it is greater than one-tenth of the film thickness, and the surface with longitudinal pattern affects the load capacity most. However, surface roughness has less effect on lubrication results than lubricants' non-Newtonian property.