Microwave-assisted aqueous two-phase extraction (MAATPE) was applied to simultaneous extraction of diverse polysaccharides from Lentinus edodes with aqueous two-phase extraction system (ATPS) of ethanol/ammonium sulfate as the biphasic extractant. Key factors in MAATPE process were optimized by response surface methodology, and the optimum conditions were concluded as follows: the ATPS composition of ethanol concentration 26.0% (w/w) and (NH4)2SO4 concentration 19.58% (w/w), extraction temperature 78.7 °C, extraction time 19.55 min and solid-to-solvent ratio 1:50. The extraction yields of the polysaccharides from the top phase (PTP) and the bottom phase (PBP) were 2.12 ± 0.21% and 11.16 ± 0.28%, respectively. By means of FT-IR, HPGPC and HPLC analysis, PTP and PBP were different from each other in chemical structure, their average molecular weight (MW) were respectively 119,533 Da and 3906 Da. Also, the mechanism of MAATPE process was explored by composition analysis and scanning electron microscopy. Both polysaccharides exhibited stronger antioxidant activities, EC50 values of scavenging DPPH, hydroxyl and superoxide radicals for PBP achieved 580 ± 3, 83.1 ± 3.6 and 91.1 ± 0.5 μg/mL as against 560 ± 4, 76.3 ± 2.2 and 89.3 ± 2.4 μg/mL of PTP, respectively. Compared with conventional methods using a mono-phase solvent, MAATPE can not only greatly improve extraction efficiency, but also selectively extract diverse polysaccharides.