Prebiotic xylooligosaccharides (XOS) are derived from xylan-rich agricultural residues and have important applications in the food, pharmaceutical, and cosmetic fields. The high hygroscopicity and low glass transition temperature (Tg) of XOS could result in operating problems and deterioration of product quality during the drying process and storage, so it is important to enhance physicochemical properties of dried product for improve XOS quality. The objectives of this work were spray drying XOS and comprehensive studying their rheological properties, physicochemical, and morphological characterization, when carried by gum Arabic (GA). The antioxidant effects of the products were evaluated by 2,2-Diphenyl-1-picrylhydrazyl (DPPH), 2,2′-Azinobis (3-ethylbenzothiazoline-6-sulfonic acid ammonium salt) (ABTS+), ferric reducing antioxidant power (FRAP), and oxygen radical absorbance capacity (ORAC). The intuitive perturbation plot was applied to analyse the effects of the independent variables on the responses. A polynomial equation and the Gordon-Taylor equation were used to model the experimental data, and the fitted equations revealed the powder quality and storage stability well (R2> 0. 95). The molecular weight of the carbohydrate affected the rheological properties and Tg. Increasing the solid content of the initial solution tended to increase the apparent viscosity and median diameter. The EC50 values of representative products were 1126.00 and 651.69 μg/mL by DPPH and ABTS+ assays, and antioxidant activity values of representative products were 49.68 and 64.95 μmol TE/g by FRAP and ORAC assays, which shown the remarkable antioxidant effects. The drying yield, hygroscopicity, Tg, microencapsulating efficiency, and colour attributes (L*, a*, and b*) of representative high GA concentration (GAC) products were 76.10%, 13.00 g H2O/100 g dry weight, 71.10°C, 99.69%, 96.93, 1.13, and 3.66, respectively, which shown better quality properties than low GAC products. According to the X-ray diffraction and scanning electron microscopy analysis, the microparticles were amorphous, and well-separated under an appropriate GAC. The Fourier transform infrared spectra results shown that the XOS and GA preserved their structural integrity during the spray drying process.