The invention belongs to the technical field of biology, and relates to a multiplex amplification system for rapidly mutating Y-chromosome short tandem repeats, a kit and an application. The multiplexamplification system comprises 16 pairs of primers, and can be used for amplifying 16 STR loci: DYS630, DYS464, DYF403S1b, DYF399S1, DYS518, DYF403S1a, DYS527, DYS713, DYS612, DYS626, DYS627, DYS526,DYF404S1, DYF387S1, DYS449, and DYS547. Compared with prior art, the system is advantageous in that: 1. the system contains 16 human male Y-chromosome high-mutation rate STR, and the system is uniqueand novel with a large amount of information content and good compatibility; 2. the system has wide application range, good directivity, and high precision, and the system is suitable for legal medical expert DNA analysis in material evidence cases which relate to all cells of male; wherein biological testing materials which contain mal cells, such as bloodstain, seminal stain, saliva, hair, nail, cartilage and other human tissues, can be identified. 3. the system has good system specificity and good stability, multiple repeat checking is not needed, non-specific amplification products are not generated, and signal intensity is stable; 4. the system has high sensitivity, and DNA template amount which is low to 15pg can be accurately classified.