Feature extraction is a very important step in Synthetic Aperture Radar automatic target recognition (SAR ATR). In this paper, a feature extraction procedure based on the nonnegative matrix factorization (NMF) and Fisher linear discriminant (FLD) analysis is proposed for target recognition in SAR images. Firstly, segmented SAR images are processed by the NMF algorithm, which can extract nonnegative features that contain the local spatial structure information of targets. Then the FLD method is applied to the extracted features, thus the discriminability of the features can be enhanced. Both the spatial locality and separability between classes are enforced by this two-phase feature extracting procedure. Finally, the obtained features are used for automatic target recognition. Compared to several other methods, experimental results show the effectiveness of the proposed method for target feature extraction and recognition in SAR images.