The invention provides a method and system for individual recognition and paternity identification of an unknown sample. The method includes: extracting the DNA of the unknown sample; acquiring the typing result of 17 loci contained by the DNA, i.e. 14 autosome STR loci, 2 Y-chromosome loci, and the sex determination locus Amelogenin, with the STR loci being D6S1043, D21S11, D7S820, CSF1PO, D2S1338, D3S1358, D13S317, D8S1179, D16S539, Penta E, D5S818, vWA, D18S51 and FGA, the Y-STR locus being DYS448, and the Y-chromosome insertion/deletion site being M134; and carrying out individual recognition and paternity identification according to the genotypes of the 17 loci of the unknown sample. The invention also provides the system for individual recognition and paternity identification of the unknown sample. The scheme involved in the invention can realize simultaneous detection of autosome STR loci and Y-chromosome loci, and also can shorten the detection time, thus improving the efficiency of individual recognition.