Machining systems have been evolved to produce more detailed products of high added value. This has been possible, in large part, due to the development of highly accurate multi-axis CNC machine tools. The conventional CNC of machine tools has individual axis controllers to maximize tracking performance. On the other hand, cross-coupling controllers can be integrated into the conventional CNC to enhance contouring performance. For this multi-axis cross-coupling control system, it is necessary to automatically adjust the controller gains depending on operating conditions and/or other external conditions from an optimization perspective. This paper proposes automatic modeling of feed drive systems that minimizes the difference in behavior between the system model and the actual system. Based on the modeling, an integrated auto-tuning method is also proposed to improve both tracking and contouring accuracy of a 3-axis cross-coupling control system as well as users’ convenience. The proposed methods are evaluated by both simulation and experiments.