Isotope analysis is important method for confirmation element component of compounds in low resolving mass spectrum. When using isotope analysis, the abundance of isotope must be correctly measured, and the mass charge rate(m/z) of isotope must be different from other fragments, namely the abundance of isotope only producing by itself. This condition is very difficult to come true actually, in most case the m/z of the other fragments is the same with isotope. In this article a method was proposed, which can solve the problem and give the correct result of element of compounds with the analysis and calculation a few different fragments and isotopes.