Objective: This study aimed to optimize the microwave assisted aqueous two-phase extraction (MATPE) process of polysaccharides from Cornus officinalis and obtain a uniform polysaccharide fraction. Methods: The best extraction technology was determined through an orthogonal experiment. To obtain a uniform polysaccharides fraction (COP-2-S), the crude extract of C. officinalis polysaccharides was purified using DEAE-52 cellulose and Sephadex G-100 column chromatography. The molecular weight of COP-2-S was determined by high performance gel permeation chromatography. The monosaccharide composition of COP-2-S was determined by gas chromatography. The structure of COP-2-S was characterized by UV, and IR spectra, and a scanning electron microscope. Results: The optimal MATPE process of polysaccharides from C. officinalis was as follows: microwave power of 300 W, ethanol volume fraction of 35%, ammonium sulfate mass fraction of 22%, a solid-to-liquid ratio of 1∶20 (g/mL), and the yield of polysaccharides from C. officinalis was (12.04±0.17)%. The molecular weight of COP-2-S was 17 450 Da. The molar ratio of arabinose, glucose, and galactose that made up the monosaccharide was 12.85∶30.71∶18.09. Conclusion: COP-2-S had no characteristic absorption at 260 nm and 280 nm. Besides, COP-2-S had typical infrared absorption characteristics of polysaccharides.