The isotopic compositions of cosmic ray nuclei are of great interest since they directly reflect processes related to cosmic ray propagation through the galaxy. In six years of data taking, AMS has collected the largest available data set on fluxes of nuclei. For a selected nuclear charge value, the velocity and rigidity give a measurement of particle mass that allows measurement of relative isotopic abundances. The AMS Ring Imaging CHerenkov (RICH) detector provides particle velocity measurements with resolution better than 0.1%, whereas the silicon tracker provides rigidity determination through the measurement of particle's trajectory in the magnetic field of AMS. In this contribution, we present the methodology used to obtain the isotopic composition of helium nuclei with AMS.