In the micro-milling process, cutting thickness always changes dynamically, which may cause chatter. The key to good surface quality is the minimization of tool chatter. This requires an understanding of the milling tool and the milling structure system dynamics. Frequency response function (FRF) at micro-milling tool point reflects dynamic behavior of the whole micro-milling machine-spindle-tool system. In this paper, based on receptance coupling substructure analysis(RCSA) and considering rotational degrees of freedom, tool point frequency response function of micro-milling dynamic system are obtained by coupling two kinds of functions calculated by Timoshenko's beam theory and Euler's beam theory and obtained by hammer testing. And frequency response functions solved by different beam theories are compared. Finally, the frequency response function is identified as the modal parameters, and the modal parameters are transformed into equivalent structural parameters of the physical system. The research work provides base for the dynamic study of the micro-milling system.