As molecular weight controls the biological activities of polysaccharides, screening the optimal molecular weight of polysaccharides is important in drug research and application. In this study, hydrogen peroxide was employed as oxidant, and temperature, reaction time, and concentration of polysaccharides and hydrogen peroxide were examined for their effects on the preparation of polysaccharides in different molecular weights from Ulva pertusa. Our experiment suggested that the optimal degradation concentrations for polysaccharides and hydrogen peroxide were 2.5% (w/v) and 8.0% (v/v), respectively. The range of degradation measured by relative viscosity was mainly controlled by temperature and time. Results revealed that 35℃ was the optimal temperature for obtaining low-degradation samples, and 50℃ was the most favorable temperature to accelerate the reaction to yield highly-degraded samples. Four samples in different molecular weights A, B, C and D were finally prepared. The controllability was evaluated by the relative standard deviation (RSD) of relative viscosity, and the peak molecular weights and the polydispersity indexes (Mw/Mn) of molecular weights were measured by high performance gel permeation chromatography (HPGPC).