In order to achieve the aim of automatic balancing of air bearing spindles, the imbalance-induced vibrations need to be measured first. However, the measured signals are usually contaminated with harmonic error motions and noise. In this paper, an adaptive approach is proposed for the separation of unbalance vibration in air bearing spindles. The fundamental error motion, high-order harmonic error motions and noise are separated adaptively with the complementary ensemble empirical mode decomposition (CEEMD) method. The vibrations under the excitation of different unbalance masses are measured and analyzed at various rotating speeds. The results are beneficial for the accurate estimation of unbalance mass in air bearing spindles.