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Nonnegative matrix factorization (NMF) is widely used in signal separation and image compression. Motivated by its successful applications, we propose a new cryptosystem based on NMF, where the nonlinear mixing (NLM) model with a strong noise is introduced for encryption and NMF is used for decryption. The security of the cryptosystem relies on following two facts: 1) the constructed multivariable nonlinear function is not invertible; 2) the process of NMF is unilateral, if the inverse matrix of the constructed linear mixing matrix is not nonnegative. Comparing with Lin's method (2006) that is a theoretical scheme using one-time padding in the cryptosystem, our cipher can be used repeatedly for the practical request, i.e., multitme padding is used in our cryptosystem. Also, there is no restriction on statistical characteristics of the ciphers and the plaintexts. Thus, more signals can be processed (successfully encrypted and decrypted), no matter they are correlative, sparse, or Gaussian. Furthermore, instead of the number of zero-crossing-based method that is often unstable in encryption and decryption, an improved method based on the kurtosis of the signals is introduced to solve permutation ambiguities in waveform reconstruction. Simulations are given to illustrate security and availability of our cryptosystem.