The effects of low viscosity chitosan on the rheological properties of soymilk using a model system and on tofu qualities were examined. The flow behavior of soymilk with chitosan closed the Newtonian flow and stabilized according to increasing chitosan concentration. The soymilk containing glucono-δ-lactone exhibited a more pseudoplastic flow behavior compared with that of the control soymilk. The addition of low viscosity chitosan to the tofu preparation did not significantly affect its physicochemical properties. However, the results of the TEM image and instrumental textural properties showed that low viscosity chitosan affected the construction of the tofu structure. Chitosan tofu had low scores across the whole field of appearance in the sensory evaluation, and its overall eating quality was scored significantly lower. These results suggest that the addition of low viscosity chitosan affects the quality of tofu, which changes according to the degree of polymerization and concentration of chitosan.