The invention discloses a measurement method of an inorganic nitrogen isotope fractionation value of an ammonium salt assimilated by a plant. Clonal tissue culture seedlings are cultured in culture media, in which two kinds of nitrate with different stable nitrogen isotope values serve as sole nitrogen sources, respectively; after the tissue culture seedlings are cultured for 5 weeks, the stable nitrogen isotope values of leaves of the tissue culture seedlings cultured under the two kinds of nitrate are measured; similarly, clonal tissue culture seedlings are additionally taken, and are cultured in culture media with mixed nitrogen sources formed by the ammonium salt and the two kinds of nitrate whose stable nitrogen isotope values are different respectively; the stable nitrogen isotope values of the leaves of the tissue culture seedlings cultured under the two mixed nitrogen sources are measured; shares, which are utilized by the tissue culture seedlings, of the nitrate are calculated, and accordingly, afterwards, the stable nitrogen isotope values after the ammonium salts assimilated by the tissue culture seedlings cultured under the mixed nitrogen sources generate nitrogen isotope fractionation are calculated; finally, the stable nitrogen isotope fractionation values generated by the ammonium salts assimilated by the tissue culture seedlings, namely, to-be-measured stable nitrogen isotope fractionation values generated by the ammonium salts assimilated by the plants, are obtained. The measurement method can measure the inorganic nitrogen isotope fractionation value of the ammonium salt assimilated by a plant which cannot grow due to monoammonium or a plant which grows under the mixed nitrogen source; as a culture experiment is developed by utilizing the clonal tissue culture seedlings of the same genotype, the measurement result is more reliable.