According to the characteristics of color image encryption, in order to reduce the correlation of images, increase the key space and improve the security, the color image encryption algorithm based on DNA sequence operation and fractional order Chen hyper-chaotic system is proposed. The three-dimensional color image is transformed into three two-dimensional DNA sequence matrices. The chaotic sequences which is generated by fractional order Chen chaotic system are used to scramble the locations of elements from three DNA sequence matrices, and then divide three DNA sequence matrices into some equal blocks respectively. The proposed algorithm adds these blocks by using fractional order Chen chaotic system and DNA sequence addition operation. The encrypted color image by decoding the DNA sequence matrices and recombining the blocks. The simulation results and security analysis show that the proposed algorithm has the advantages of low space, short time, low correlation, big space of the key, high sensitivity of the key, high security and strong resist attacks ability compared with other image encryption algorithms.