The modified average Reynolds equation for friction pairs with arbitrary three-dimensional rough surfaces lubricated by couple stress fluid is derived by the average flow method. And the performance parameters under the effect of couple stress, surface roughness, journal misalignment, and thermal effect are obtained with the finite difference numerical method. The surface roughness factor plays an important role even though the nominal eccentricity ratio is small. With the increase of the nominal eccentricity ratio, the greater values of the couple stress parameter, the greater values of performance parameters except for the dimensionless maximum oil film temperature and the dimensionless friction power. With the increase of the degree of misalignment, the greater values of the couple stress parameter, the greater the dimensionless maximum average film pressure, the dimensionless load capacity, and the dimensionless misalignment moment. As the value of the couple stress parameter is increased, the greater values of the dimensionless surface roughness, the greater values of the performance parameters except for the dimensionless side leakage. This research can widely use in various forms of friction pairs such as thrust bearings, sliding bearings, piston ring-cylinder liners.