The invention discloses a water-based positive electrode polymer, a preparation method thereof and a small molecule flow battery system, the water-based positive electrode polymer is synthesized by free radical polymerization of 2-methyl-2-acrylic acid-2, 2, 6, 6-tetramethyl-4-piperidine methyl ester (TEMPMA), 3-sulfonic acid propyl potassium methacrylate (SMPS) and 2-methyl-2-propylene-1-sodium sulfonate (SMAS), and the water-based positive electrode polymer is obtained by polymerization of the free radical polymerization of 2-methyl-2-acrylic acid-2, 2, 6, 6-tetramethyl-4-piperidine methyl ester (TEMPMA), 3-sulfonic acid propyl potassium methacrylate (SMPS) and 2-methyl-2-propylene-1-sodium sulfonate (SMAS). The micromolecule flow battery system comprises the aqueous positive electrode polymer and 1, 1-dimethyl-4, 4-dipyridyl dichloride. The polymer is used as an electrode material, on one hand, the increase of molecular weight can effectively reduce cross contamination among active substances, and decrease of battery capacity is reduced; and on the other hand, the porous membrane with lower cost can be directly used, so that the use cost is reduced. By adopting the polymer electrolyte with high concentration and low viscosity, the concentration polarization phenomenon can be inhibited, the stability of the battery is improved, the flow battery with the advantages that the active material is easy to prepare, the capacity is high, the safety performance is high, the charge-discharge performance is stable and the like is obtained, and the large-scale energy storage requirement is met.