The targets of speech separation, whether ideal masks or magnitude spectrograms of interest, have prominent spectro-temporal structures. These characteristics are very worthy to be exploited for speech separation, however, they are usually ignored in previous works. In this paper, we use nonnegative matrix factorization (NMF) to exploit the spectro-temporal structures of magnitude spectrograms. With nonnegative constrains, NMF can capture the basis spectra patterns of speech and noise. Then the learned basis spectra are integrated into a deep neural network (DNN) to reconstruct the magnitude spectrograms of speech and noise with their nonnegative linear combination. Using the reconstructed spectrograms, we further explore a discriminative training objective and a joint optimization framework for the proposed model. Systematic experiments show that the proposed model is competitive with the previous methods in monaural speech separation tasks.