More and more people having cell phone, they must pay more attention to message security of their personal privacy, in which cell phone short message security is the most important. In this paper, we focus on designing an encryption hardware system of cell phone short message with chaos and A5/1 hybrid algorithm and realizes it on field programmable gate array. In the encrypted core, chaotic sequences of logistic map are used as initial keys of A5/1 algorithm for encrypting short messages, and in this paper we prove the relationship between linear correlation and circle correlation in the pseudo-randomness research of chaotic sequences serving as the initial keys. The SIM300 modules are used to realize cell phone functions, simulate short messages of common cell phone and the encrypte short messages after processing by our system by wireless transmitting through the base station. In addition, in this paper we design a software test platform, and it can show the results of this hardware system on computer. The test results indicate that the proposed system and its hardware implementation can encrypt/decrypt short messages and ensure their normal transmission, which can improve the security of short message and ensure its integrity and reliability during transmitting.