The present invention relates to a mass measurement system and method capable of precisely measuring the mass of a sample in a gravity-free environment. The mass measurement system using measurement of frequency shift of a vibrator according to the present invention includes a vibrator vibrating at a predetermined resonance frequency with a mass of a sample added thereto, a frequency counter for measuring a resonance frequency of the vibrator caused by vibration, a standard mass database for storing therein known standard masses and standard mass frequency shifts corresponding to variation in the standard masses, and a main controller for calculating a sample mass frequency shift corresponding to the added sample mass on the basis of the resonance frequency received from the frequency counter, searching the standard mass frequency shifts stored in the standard mass database, comparing the calculated sample mass frequency shift with the searched standard mass frequency shifts, extracting a predetermined standard mass, outputting the extracted standard mass as the mass of the sample, and controlling the entire system. Accordingly, the present invention can precisely measure the mass of a small-sized sample, in particular, an animal sample, in a gravity-free environment.