The cylinder liner bears alternating thermal load and mechanical load, and evaluating the cylinder liner deformation is a key issue in the design stage of an engine. In this work, the shape and position tolerance of the cylinder liner to various loads were studied based on the finite element method, the simplex algorithm and the least square method. Firstly, the heat transfer boundary conditions of the cylinder liner were obtained through combustion simulation. Combined with the mechanical load, the transient deformation of the cylinder liner under the thermo-mechanical load was obtained. Subsequently, the out-of-roundness and coaxiality were selected to evaluate the shape and position changes in the cylinder liner. Finally, the transient tolerance analysis of the cylinder liner under alternating thermo-mechanical load was carried out. The results show that the maximum out-of-roundness of the cylinder liner under thermal load, mechanical load and thermos-mechanical load was 15.12, 43.40 and 51.76 μm, respectively. The maximum coaxiality under thermal load, mechanical load and thermos-mechanical load were 6.17, 80.49 and 80.22 μm. The side thrust was more likely to cause uneven deformation of the cylinder liner section, the liner coaxiality was mainly affected by the cylinder burst pressure, and the liner shape tolerance was much more sensitive to the mechanical load than the mechanical load.