The effects of typical machining errors on the dynamic features of rod-fastened rotor bearing system (RBS) are studied in this paper. Three micron-sized machining errors are considered in a three-dimensional (3D) rod-fastened model. The static effects of machining errors are investigated by applying finite element method. Results demonstrate that machining errors not only bring about mass eccentricity but also cause obvious rotor bending due to large pretightening force. Then, nonlinear dynamic features such as stability and bifurcation are analyzed by using target-shooting technique, track-following method, and Floquet theory. Analysis data indicate that rotor bending originated from machining errors reduces the system stability evidently. It is also observed that the vibration value continues to go up after critical speed as rotating speed increases. It is a particular property compared with integral rotor. It explains the reason why the machining precision of rod-fastened rotor is much higher than that of the corresponding integral rotor to some extent. Moreover, differences between machining errors are compared and the results show that the machining precision of axial assembly interfaces should be paid more attention in the rod-fastened rotor design.