The single atom counting rate of a rare isotope and the loading rate of another stable isotope with an abundance over 10 orders of magnitude larger are measured in one atom trap. The linear correlation between the measured counting/loading rates is examined to determine the (84)Kr/(82)Kr and (85)Kr/(83)Kr ratios of a Kr gas sample. Experiments show that the relative uncertainty is reduced to 1.3% when the single atom counting rate of (85)Kr is normalized by the measured (83)Kr loading rate. The measurement of the normalized single atom counting rate can be used to determine extremely low (10(-16)-10(-11)) isotope abundance. This normalization method is robust and can also be applied in other atomic systems.