The invention relates to the technical field of synthesis of carbon isotope marker compounds and in particular to a method for preparing carbon isotope markers bisphenol S and bisphenol AF. The method provided by the invention is easy in reaction raw material obtaining, low in toxicity and simple in preparation process, and because of an expensive raw material marker phenol, a condition that an excessive amount of phenol is required in a conventional synthesis method is broken through in trace synthesis. Meanwhile, the method provided by the invention is simple in synthesis step, the synthesis method has universality, the carbon isotope markers bisphenol S and bisphenol AF can be efficiently and easily synthesized in a trace amount manner, the radioactivity purity of a target compound is up to 98%, and conditions are provided for operation that fates of degradation, conversion and the like of bisphenol S and bisphenol AF in the environment are researched by using a 13C and 14C isotopic tracer technique later.