With the development of high-strength marine diesel engines, piston skirt lubrication plays an increasingly important role. In this study, to ensure that the mixed lubrication can be applied, the contact of the PS corner and CL is simplified to a spring–damper system. A coupled dynamical–tribological numerical model of a piston skirt is proposed by combining mixed lubrication and the secondary motion of the piston. The model is then used to study how the thermal effect of the piston skirt-cylinder liner friction pair affects (i) the secondary motion of the piston, (ii) the contact force of the piston-skirt corner points, and (iii) the lubrication characteristics, while considering ring friction, friction moment of piston pin and three-dimensional thermal deformation of the piston and cylinder liner. The results show that the secondary motion under the thermal condition is less than that under the cold condition, and the reverse rotation of the piston under the thermal condition occurs earlier. Asperity contact and corner points contact appear under the thermal condition, and the friction mean effective pressure under the cold condition is 47.7% greater than that under the thermal condition. Overall, it is necessary to consider the thermal effect of the piston skirt-cylinder liner friction pair.