It is a challenging work to design a robust halftone image watermarking scheme against desynchronization attacks. In this paper, we propose a feature-based digital watermarking method for halftone images with low computational complexity, good visual quality and reasonable resistance toward desynchronization attacks. Firstly, the feature points are extracted from host halftone image by using multi-scale Harris–Laplace detector, and the local feature regions (LFRs) are constructed according to the feature scale theory. Secondly, discrete Fourier transform (DFT) is performed on the LFRs, and the embedding positions (DFT coefficients) are selected adaptively according to the magnitude spectrum information. Finally, the digital watermark is embedded into the LFRs by quantizing the magnitudes of the selected DFT coefficients. By binding the watermark with the geometrically invariant halftone image features, the watermark detection can be done without synchronization error. Simulation results show that the proposed scheme is invisible and robust against common signals processing such as median filtering, sharpening, noise adding, and JPEG compression, etc., and desynchronization attacks such as rotation, scaling, translation (RST), cropping, local random bend, and print-scan, etc.