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The nonlinear filter Boolean function of LILI-128 stream cipher generator is studied in this paper. First we measure the complexity of the stream ciphers sequence of LILI-128 stream cipher generator and obtain the shortest bit stream sequence reconstructed Boolean function of nonlinear filter in LILI-128 stream cipher generator. Then the least nonlinear Boolean function of generating stream cipher sequence is reconstructed by clusterig, nonlinear predictive and nonlinear synchronization from shortest bit stream sequence. We have verified the correctness of our reconstruction result by simulating the block diagram of Lili-128 keystream generator using our getting Boolean function and implement designers’ reference module of Lili-128 stream cipher public online, and two methods produce the same synchronous keystream sequence under same initial state, so that our research work proves that the nonlinear Boolean function of LILI-128 stream cipher generator is successfully broken.