The high-speed motorized spindle has been wildly used in the field of aerospace processing, due to its advantages such as high speed, high precision, and high efficiency. CNC machine tools used for processing aerospace products require high machining accuracy, and once the spindle fails, it will seriously affect the quality of product processing. Thus, it is important to study the faults of the spindle, especially the faults caused by subtle errors. In this work, a dynamic model of a spindle with unbalanced mass fault and spindle inclination fault is established, and the natural frequencies and mode shapes of the motorized spindle are calculated by using the whole transfer matrix method (WTMM). The deflections of the spindle initial end in the different situations are discussed when the two faults happen independently. The results show that the spindle end deflection of the same fault has different sensitivity at different speeds. At the third order of natural frequencies, the deflection of a motorized spindle is greatest regardless of the fault that occurs. Although the motorized spindle rotates at the same speed, different faults could cause different mode shapes. At the lower speed, when the unbalanced mass fault happens, the mode shape is in an arched shape, and while the spindle inclination fault happens, the mode shape is in a concave shape.