Background: Spindle imbalance vibration of the computer numerical control grinding machine may result in dramatic effects on tool wear, surface finish, and form-holding of the products, which makes the balancing procedure very essential during their manufacturing process. Although the spindle residual vibration in a single direction can be suppressed effectively by the commonly used commercial balance systems, some real-world application results show that most of these balance systems cannot reduce the spindle residual vibration in horizontal, vertical, and axial direction simultaneously. Methods: To overcome this issue, the limitation of commonly used influence coefficient method–based spindle balance method is discussed first. After that, a novel balance method is experimentally proposed for the spindle vibration control using the position fluctuation information between the carriage and guideway of the servo-axis. In this method, the position fluctuation information between the carriage and guideway and the key phase information are practically measured using the built-in linear scale and spindle servomotor encoder, respectively, in which the position fluctuation information between the carriage and guideway can be considered as an integrated representation of the spindle imbalance vibration. Combined with the influence coefficient method, the imbalance vibration presenting in the horizontal, vertical, and axial direction of the spindle can be suppressed simultaneously and effectively. Results and Conclusions: A field balancing experiment is carried out on a high-precision computer numerical control gear grinding machine. Experiment results demonstrate that, compared with the commonly used commercial balancing system, the proposed method can not only reduce the residual vibration amplitude at the objective balancing speed effectively but also reduce the residual vibration amplitude more than 50% simultaneously in each direction during the whole run-down process.