In this study, the microwave energy, known as a green and natural energy, was used for the extraction process. Therefore, the extraction system was initially designed and then the alginate and fucoidan were extracted from the brown seaweed during a biorefinery process. In order to investigate the effect of the process on the physicochemical properties of polysaccharides, the optimization design was performed using the response surface method and the optimal of microwave were compared with the conventional method. process variables studied were microwave power, temperature, extraction time, and solvent to algae ratio. The investigated responses were alginate extraction efficiency, fucoidan extraction efficiency, alginate uronic acid content, alginate emulsification activity (E24), the intrinsic viscosity of alginate, alginate, and fucoidan dpph radical scavenging activity and alginate total phenolic content. Antioxidant activities were investigated on the basis of the DPPH assay. At optimum microwave condition, the alginate and fucoidan extraction efficiencies were 39.31 and 3.71%, respectively which was significantly higher than the conventional extraction method (24.46 and 2.35%). The effect of microwave power on the extraction efficiency of alginate and fucoidan was quadratic. The effect of microwave power on the Fucoidan was higher. As the temperature and duration of the process increased, alginate and fucoidan extraction efficiency also increased. The relatively long extraction time can lead to thermal degradation of polysaccharides. The process time also had a quadratic effect on fucoidan yield, which indicates that fucoidan is more sensitive to thermal degradation. Uronic acid is reported as an index of purity of alginate. The effect of temperature, microwave power and duration of extraction on uronic acid was quadratic. In fact, excessive increase in temperature can lead to the destruction of the polysaccharide structure and break it into shorter chains and also reduce molecular weight. The extraction time also had a quadratic effect similar to the temperature on the uronic acid, and the longer the extraction resulted in degradation of the alginate. In the conventional extraction procedure, the purity of alginate was 58.48%, while this value was obtained for alginate at optimum microwave point of 62.33%. Alginate emulsifying activity is one of its most important properties in the food industry, so the effect of process conditions on alginate emulsifying activity was investigated. The effect of power, time and temperature was quadratic. By increasing the microwave power, the alginate emulsifying activity increased in both sunflower oil and olive oil systems, while at a power of 500 Watts, the incremental trend decreased slightly. This suggests that long periods of heat and wavelengths reduce the ability of alginates to form emulsions. The emulsifying activity of alginate extracted by microwave showed a significant increase. Key Words Seaweeds, Macroalge, Alginate, Fucoidan, Extraction, Microwave, Optimization, Antioxidant, Emulsyfier