Threeoligosaccharides, namely single clove garlic (SGOS), purple garlic (PGOS), and Cangshan hybrid garlic (HGOS), were prepared by water extraction and ethanol precipitation. The chemical composition and molecular weight of garlic oligosaccharides were elucidated by gas chromatograph, high-performance liquid chromatography,Fourier-transform infrared (FTIR), and nuclear magnetic resonance (NMR) analyses. Moreover, fortified dough was prepared by adding garlic oligosaccharides at different proportions to evaluate the interaction of the obtained oligosaccharides with gluten proteins. Additionally, the microcosmic, mesoscopic, and macroscopic characteristics of the fortified dough were investigated in terms of the physical and rheological properties, thermodynamic parameters, moisture distribution, morphology, and protein secondary structure using texture profile analysis, rheology, differential scanning calorimetry, low-field NMR, scanning electron microscopy, confocal laser scanning microscopy and FTIR analyses. The results indicated that SGOS was mainly composed of galactose. SGOS fraction had a slightly higher molecular weight (3.00 × 103 Da) compared to the HGOS and PGOS fractions (2.90 × 103 Da), which showed the most compatibility with the dough matrix, thereby improving the dough quality. The present study results can provide a theoretical basis for the application of garlic oligosaccharides in the development of flour-based products.