To address the practical need for maintaining and monitoring the accuracy of rotary tables during long-term operation, this paper proposes an online accuracy monitoring method based on the rotary table′s own signals. Using the positioning accuracy A and repeatability R defined by ISO230-2 as the core monitoring indicators, a mapping model from the circumferential positioning deviation ε(θ) of the rotary table to the monitoring indicators is established. By analyzing the phase relationship of signals output by the dual reading heads and combining it with the Fourier Transform, the circumferential positioning deviation is separated automatically and accuracy indicators are calculated online. On this basis, an online monitoring system based on ZYNQ is designed and implemented, and theoretical analyses were conducted and solutions were proposed for two key issues: signal synchronous acquisition and optimal harmonic order selection. An experimental platform is built, using an autocollimator and a multi-face prism as the reference system. First, the harmonic residuals separated by the online monitoring system are analyzed to determine the current optimal harmonic order. Then, the positioning deviation is separated through Fourier Transform. Experiments show that the positioning deviation obtained by this method is highly consistent with those obtained by the reference device, with a separation accuracy better than 2.10″, validating the accuracy of the positioning deviation separation method. Furthermore, by applying loads to change the accuracy state of the rotary table, when the load gradually increases from no load to 5 kg, the system can effectively monitor the change in positioning accuracy from 289.40″ to 292.70″ and repeatability from 0.23″ to 0.38″, indicating that the self-developed system can monitor accuracy changes at the 0.01″ level. This confirms the feasibility and accuracy of the proposed method for real-time and effective monitoring of accuracy during rotary table operation.