The invention discloses a self-association fracturing fluid system with a water control function and a preparation method thereof. According to the self-association fracturing fluid system, a cationic polymer is adopted as a thickening agent, an anionic surfactant is adopted as a cross-linking agent, after a cross-linking system of the cationic polymer and the anionic surfactant acts with a corresponding gel breaker, a macromolecular chain segment of the cationic polymer is broken, and is changed from a high molecule to a small molecule, and a small-molecule cationic polymer solution with a certain concentration is formed; such a small-molecule cationic polymer solution can generate strong adsorption in a stratum, thus, the wettability of the stratum is changed, the rock surface of the stratum is changed to have a highly hydrophilic nature, and the attachment energy and the flow resistance of water are increased, and water controlling and water lowering effects are achieved; the preparation method of the self-association fracturing fluid system is simple, is mild in reaction condition, is convenient to operate, and is easy for industrialized production.