The invention provides a synthesis method and application of a water soluble chitosan-based flocculant. The method comprises the steps of adding chitosan into acid solution, adding acylated monomer aqueous solution into the acid solution, uniformly stirring and mixing, performing vibration reaction for 1 to 10 h at 5 to 60 DEG C, performing precipitation and purification through ethyl alcohol and acetone, drying, and obtaining N-acylated chitosan; sequentially adding the N-acylated chitosan, deionized water, acrylamide and strong cation functional monomer into a reactor, uniformly stirring, leading nitrogen into homogenous solution to remove oxygen, adding a photoinitiator and a cosolvent, uniformly stirring and mixing, putting the raw materials into an ultraviolet light reaction device to perform polymerization reaction, drying, performing granulation and powder process, and obtaining the water soluble chitosan-based flocculant; the flocculant can be used for the removal treatment of alga in source water. The flocculant is good in solubility property, high in viscosity coefficient and short in synthesis time, does not need temperature reduction control, simplifies the production technology, reduces energy consumption, and reduces the production cost.