In order to estimate the origin and resident time of groundwater, the helium isotope ratio (3He/4He) should be analyzed precisely. We present here experimental details of an analytical system including a helium purification vacuum line, the purification procedure, and the adjustment of a noble gas mass spectrometer. A resolving power of about 550 at the 5% level of the peak height was attained for the complete separation of 3He ions from those of HD and H3. The reproducibility of the helium isotope ratio was about 1%, examined by repeated measurements of an air standard. The accuracy of the ratio was checked by comparing observed data with reports in the literature. The results show that it is possible to apply the present system to geohydrology.