In this paper, the tool-tip responses for ball end milling, due to the coupling effects of a flexible rotor-bearing system, are investigated numerically. The milling machine tool spindle is modelled as the flexible rotor-bearing system. The critical speeds, natural modes, and unbalance responses of the system are calculated by applying the generalized polynomial expansion method. This generalized polynomial expansion method expresses the displacement as a series formed by the product of generalized coordinates and axial coordinate polynomials. According to the dynamic cutting force obtained by some scholars in the past, combined with the characteristics of the flexible rotor, the dynamic response of the tool-tip for ball end milling is numerically analyzed. The responses, including time histories, orbits, and FFT diagrams, are plotted to analyze the dynamic behaviors of the tool-tip. The coupling effects of the flexible rotor-bearing system on the system for ball end milling are first studied using the generalized polynomial expansion method. Unlike previous studies, the natural frequency varies with spindle speed and which of the different modes are included in the tool-tip response depends mainly on the spindle speed. Thanks to the gyroscopic effect, the critical speeds and responses of tool-tips can be discussed with respect to various spindle speed and tool flutes. The natural modes are accurately determined, and will excite critical speeds for certain modes, including forward and backward modes, thereby significantly affecting tool-tip response. In addition, the cutting force component associated with the tool-tip response affects the rotor-bearing system parameters, complicating the issue. Milling at higher spindle speed (2160–19,950 rpm), an important new result is found that the tool-tip oscillates with the cutting-force frequency, accompanied by a longer period vibration of the first backward mode of the rotor-bearing system. It can also be seen from the frequency spectrum analysis that, as the spindle speed increases, the peak amplitude of the first backward mode becomes larger. Milling at lower spindle speed (960, 1320 rpm), the in-plane vibration trajectory of the tool-tip gradually expands outwards clockwise around the origin until a stable loop is reached. This is because only the first backward mode of the rotor-bearing system is excited. Considering the coupling effect of the rotor-bearing system to perform the vibration analysis of the milling machine system, the parameters of the system can be designed or the spindle speed can be selected to avoid severe vibration during machining.