The invention discloses a fluorescent-labeled X-STR locus multiplex amplification system and application thereof. The system analyzes ten loci, namely DXS7133, DXS6801, DXS981, DXS7424, DXS6789, DXS7132, GATA165B12, DXS6803, DXS101, and GATA31E08 through multiplex amplification, and primers of the ten loci are labeled by four fluorescences, namely FAM, HEX, TAM, and ROX respectively. The invention can prepare a reagent kit; and as an X-STR locus multiplex amplification regent kit with distinct Chinese characteristics, the reagent kit can be used for gene location of identification in disputed paternity, individual recognition, sex appraisal and X-linked inheritable diseases, particularly for prenatal diagnosis and identification in disputed paternity such as sister relationship claim, half sister relationship claim with half blood, generation-skipping relationship claim and so on.