The invention discloses a double color image encryption method based on DNA sequence operation and deformed coupled map lattices. The method comprises: utilizing a secret key and two color plaintext images to generate parameters and initial values of iterating the deformed coupled map lattices, and generating secret key streams of L1, L2, K1 and K2 and random numbers of d1, d2 and d3 through iteration; separating red, green and blue trichromatic components of the plaintext images, transforming the components into binary matrices, and recombining the six binary matrices to obtain recombination matrices of A and B, utilizing the secret key streams of L1 and L2 to carry out bit-level scrambling on the matrices of A and B, and dividing the same into six binary matrices; utilizing a DNA encoding rule and combining the random numbers of d1, d2 and d3 to transform the binary matrices into DNA matrices, and executing DNA addition, subtraction and exclusive OR operations; and utilizing a DNA decoding rule to transform the DNA matrix into decimal matrices, utilizing the secret key streams of K1 and K2 and the bitwise exclusive OR operation to change values of image pixels, and obtaining ciphertext images of C1 and C2. The method can encrypt the two plaintext images at the same time, and has the advantages of high security, good encryption effect, no information loss, fast encryption speed and the like.