The invention provides a DNA chip based cipher system. The DNA of the DNA chip of the cipher system is a random sequence G (i, j). Oligonucleotide probes S (i, j) are oligonucleotide fragments obtained through artificially synthesizing the reverse complement sequences of a small-segment DNA sequence randomly intercepted from the random DNA sequence G (i, j) corresponding to the lattices of the DNA chip, and the uniqueness of the small-segment DNA sequence in the DNA chip is determined through using BLAST. Information encryption is that a DNA chip lattice distribution map M is marked with different G (i, j) to represent plaintext information, and then the oligonucleotide probes S (i, j) corresponding to the G (i, j) are mixed; and information decryption is that the oligonucleotide probes S (i, j) are hybridized with the random sequence DNA sequence. The encryption of same plaintext information can be realized through a large amount of different S (i, j) probe mixture combinations and can be admixed with any unlabeled DNA at will. The S (i, j) probes are composed of the random DNA sequence, and plaintext information related information is not coded in the DNA sequences of the mixtures of the S (i, j) probes, so the system cannot be decoded.