The invention belongs to the field of biotechnology, and relates to a compound amplification system, a kit and an application of rapidly mutating Y chromosome short tandem repeat sequences. The compound amplification system includes 16 pairs of primers, which can simultaneously amplify 16 STR sites: DYS630, DYS464, DYF403S1b, DYF399S1, DYS518, DYF403S1a, DYS527, DYS713, DYS612, DYS626, DYS627, DYS526, DYF404S1, DYF387S1, DYS449, DYS547. Compared with the prior art, the present invention has the following advantages: 1. Contains 16 STRs with high mutation rate of human male Y chromosome, which is unique and novel, with large amount of information and good compatibility. 2. It has wide adaptability, strong directivity and high precision, and is suitable for forensic DNA analysis in all cases involving male cellular evidence. All biological samples containing male cells, such as blood stains, semen spots, saliva, hair, nails, cartilage and other human tissues, can be identified. 3. The system has good specificity and stability. After repeated verifications, no non-specific amplification products are produced, and the signal intensity is stable. 4. High sensitivity, the amount of DNA template as low as 15 pg can be accurately typed.