Rod fastening rotor (RFR), as a typical rotor structure of gas turbine which is different from the integral rotor, is comprised of a set of discs clamped together by a central tie rod or several tie rods on the pitch circle diameters. In process of machining, tolerances of the disc are inevitable, of which the parallelism error and mass imbalance are focused on in this paper. Firstly, the complex bending of RFR by accumulation of parallelism errors of discs is derived through the coordinate transmission. Then the static analysis of RFR is performed to obtain the additional pressure by the effect of unbalanced forces, which is related to the assembly angles and rotating speed, on contact surfaces using a linear hypothesis, based on which the distribution of contact pressure considering the original pre-tightening force is obtained. Then the Bifractal-Regular theory is adopted to acquire the micro-topography of the contact interface and derive the contact stiffness related to normal contact pressure, fractal upper length limit and regular shape of the contact interfaces. After that, the zero thickness element is introduced to obtain the equivalent stiffness matrices of the contact surface. In addition, the circumferential uniformly distributed rods are modeled as a spring element which provides additional bending stiffness for the RFR. Based on the analysis above, the dynamic model of the RFR-bearing system containing 10 discs is established using the Timoshenko beam element where the continuous part of the shaft is modeled by Timoshenko beam element considering shear effect. Finally, the multi-optimization is carried out on the vibration response by the coupled effects of both initial bending and mass imbalance of the RFR-bearing system through which the optimal assembly angles are obtained. The results show a good performance in decreasing vibration as well as bending of the RFR system.