A HHT-based vibration monitoring system, consisting both of the software and the hardware system, was designed and implemented according to the non-stationary nature of the vibration signal from NC spindle. The hardware system concerns with the development of the data acquisition module based on FPGA and PC104 bus, and the software system includes both the monitoring module of time domain wave and the counterpart of the characteristic data. The function of characteristic data monitoring is divided into two parts, i.e., the spectrum distribution monitoring and the time-frequency distribution monitoring. In order to reflect the non-stationary characteristic of the vibration signal from NC spindle more accurate, a data analysis approach, named the Hilbert-Huang Transform (HHT), was introduced into the developed system. Test and analysis of the vibration signal show that the vibration monitoring system not only can characterize the time domain wave and the spectrum distribution, but also can implement the tracing of the time-frequency distribution through HHT’s superiority in characterizing instantaneous frequency.