ABSTRACT Target detection is one of the most important applications of hyperspectral technology. However, due to spectral variations caused by noise or environment, the within-class variation is enlarged which degrades the performance of detectors, especially when the target size is small. Therefore, improving the detection performance of small targets and noisy targets is a key task. Considering the great feature extraction and representation ability of deep learning models, denoising autoencoder (DAE) is introduced to reconstruct spectrums and exploit the invariant information for target detection. To fully extract the features from the original spectrums, a multiscale denoising autoencoder (MSDAE) model is designed to incorporate complementary informationin in this paper. The final spectrum is fused by reconstructed spectrums from different scales representations, which provides more complex information and more robust features for subsequent spectral identification. Results on simulated hyperspectral images (HSIs) and real-world HSIs demonstrate that the proposed MSDAE model can effectively remove noise interference and lead to great improvements of the target detection. In addition, the proposed method shows significant potential in preserving small targets.