The ultra-precision spindle is the key component of ultra-precision machine tool, which largely influences the machining accuracy. Its frequency characteristics mainly affect the frequency domain error of the machined surface. In this article, the error measurement setup for the ultra-precision aerostatic spindle in a flycutting machine tool is established. The dynamic and multi-direction errors of the spindle are real-time measured under different rotation speeds. Then, frequency domain analysis is carried out to obtain its regularity characteristics based on the measurement result. Through the analysis, the main synchronous and asynchronous errors with relatively large amplitude of the spindle errors are found, and the amplitude change law of these main spindle errors is obtained. Besides, the cause of the main synchronous and asynchronous errors is also analyzed and indicated. This study deepens the understanding of ultra-precision spindle dynamic characteristics and plays the important role in the spindle frequency domain errors’ control, machining process planning, frequency characteristics analysis and oriented control of the machined surface errors.