In the micro-milling process, the minimization of tool chatter is critical for good surface finish quality. The analysis of chatter requires an understanding of the milling tool as well as the dynamics of milling system structure. Frequency response function (FRF) at the micro-milling tool point reflects dynamic behavior of the whole micro-milling machine–spindle–tool system. However, the tool point FRF of micro-milling cannot be obtained directly through the hammering test. To solve the problem, the authors get the FRF of the spindle system based on the rotating Timoshenko beam theory and the receptance coupling substructure analysis (RCSA), and the bearing characteristics are added into the spindle model through structural modification. Then, the centrifugal force and gyroscopic effect caused by the high-speed rotation of the micro-milling spindle are considered to better simulate the real scenario and increase the accuracy of modal parameters. The method has general usage and can be applied to all the micro-milling tools under which only the spindle dimension, bearing characteristics, and contact parameters need to be changed.