In the realm of automatic wire-traction micromanipulation systems, the alignment of the central axis of the coil with the rotation axis of the rotary stage can be a challenge, which leads to the occurrence of eccentricity during rotation. The wire-traction is conducted at a micron-level of manipulation precision on micron electrode wires; eccentricity has a significant impact on the control accuracy of the system. To resolve the problem, a method for measuring and correcting the coil eccentricity is proposed in this paper. First, models of radial and tilt eccentricity are established respectively based on the eccentricity sources. Then, measuring eccentricity is proposed by an eccentricity model and microscopic vision; the model is used to predict eccentricity, and visual image processing algorithms are used to calibrate model parameters. In addition, a correction based on the compensation model and hardware is designed to compensate for the eccentricity. The experimental results demonstrate the accuracy of the models in predicting eccentricity and the effectiveness of correction. The results show that the models have an accurate prediction for eccentricity that relies on the evaluation of the root mean square error (RMSE); the maximal residual error after correction was within 6 μm, and the compensation was approximately 99.6%. The proposed method, which combines the eccentricity model and microvision for measuring and correcting eccentricity, offers improved wire-traction micromanipulation accuracy, enhanced efficiency, and an integrated system. It has more suitable and wider applications in the field of micromanipulation and microassembly.