Aiming at the alignment problem of the multi-stage turbine shafting of heavy duty gas turbines, an optimization alignment method integrating the reaction force of bearing and relative displacement between bearings was established, and a verification in hot-state was conducted. Firstly, the finite element software ANSYS Workbench was used to simulate the deformation in cold-state of the shafting, and the reaction forces and vertical displacements of the key bearings were obtained. Secondly, a multi-parameter optimization method integrating reaction force of bearing and the relative displacement between bearings was adopted, and the optimal solution was calculated by using the MATLAB software. Then, the Fluent software was used to simulate and analyze the airflow distribution between the intake volute and the shafting, the temperature influence under the actual working state of the shafting was taken into account to verify the validity of the optimal solution in hot-state. Finally, the bearing 5# was lowered by 0.057 mm in cold-state, the shafting was precisely adjusted, and an alignment experiment in hot-state was conducted. The results showed that the vibration of the shafting met the index requirements, verifying the effectiveness of the alignment scheme. The proposed shafting alignment optimization method takes into account the actual temperature and complex loads of the shafting, and has a good guiding significance for the precise adjustment of the shafting.