The nonsynchronous error of the dual-driven feed system seriously affects the positioning and machining accuracy of CNC machine tools. Improving the positioning error is an extremely important task as it determines the geometric accuracy of the manufactured parts. In this paper, a Multivariate Orthogonal Polynomial Regression model has been developed to predict the positioning error in terms of motion parameters such as position and speed of the X1 and X2 axes of the dual-driven worktable. Orthogonal Experimental Design has been engaged in conducting experiments. The positioning errors are measured by a dual-frequency laser interferometer. In addition, a real-time error compensation system is developed based on the proposed active compensation control strategy in the dual-driven feed system controlled by Beckhoff motion control card. Experimental results show that the proposed positioning error model and error compensation strategy can be utilized as an effective manner to improve the accuracy of dual-driven CNC machine tools.