The invention relates to the field of element isotope analysis, and particularly discloses an element isotope analysis system, an analysis method of sulfur isotopes in a trace sulfate sample and application of the analysis method. The system comprises an element analyzer, an enrichment device, a gas chromatographic column, an isotope ratio mass spectrometer and a heating device which are connectedin sequence, and pipelines for connecting or communicating equipment, wherein the pipeline used for connecting or communicating the equipment is a Teflon pipe, the gas chromatographic column is a chromatographic column made of a Teflon material, the enrichment device comprises a multi-way valve, a sample tube and a cooling trap, at least one part of the sample tube can be arranged in the coolingtrap to realize enrichment, and the heating device is arranged around the sample inlet, the sample inlet valve and the ion source of the isotope ratio mass spectrometer. The analysis method is simple,controllable, easy to operate, capable of utilizing the sample to the maximum extent, low in instrument detection limit, high in sensitivity, small in analysis error and high in accuracy.