The principle of balancing a high speed cantilever rotor at full speed has been put forward by low-speed and high-speed balancing. The portable field dynamic balancing instrument based on the microcontroller is discussed from the hardware, the software and the signal process in detail. With the developed instrument, the whole-machine balancing experiment was conducted on a saucer-separating centrifuge RJ-460. The vibration of the saucer-separating centrifuge decreased from 3.8mm/s to 0.3mm/s at 1200r/min and decreased from 9.8mm/s to 0.6mm/s at 7200r/min. The experimental results indicated that the principle of balance is correct and the designed instrument is reliable and promising.