To improve the system performance, precision manufacturing is required for production of the internal combustion engines (ICEs), a typical complex nonlinear system. Previous studies show that tolerances of critical dimensions have significant impacts on the engine performance. Among many critical factors, friction loss is one of the most important ones that affect the output performance of ICEs. It is necessary to recognize and control the tolerances which affect the friction loss. Of all the friction pairs for the engine, it is observed that the piston-cylinder friction pair and the bearing system take up nearly 70% of the total friction loss. In this work a novel multi-objective tolerance design optimization problem considering two friction systems mentioned above is proposed and solved. First two separated simulation models, the piston-cylinder and the bearing are built using AVL Excite Piston & Ring® and AVL Excite Power Unit®, respectively. Since there are shared dimensions in these two models, an analysis model based on Gaussian Process is proposed using the simulation results, which combines the two independent simulation models to facilitate the problem formulation and solving. Finally, the multi-objective tolerance design optimization problem is formulated and solved using a newly developed sequential multi-objective optimization (S-MOO) method.