The present invention discloses a clean fracturing fluid system and a preparation method thereof, wherein the fracturing fluid system comprises, by mass, 3-6% of a cationic surfactant, 1-4% of a zwitterionic surfactant, 0.5-1.5% of counter ion, 2-5% of an electrolyte, and the balance of water. The clean fracturing fluid preparation method comprises: mixing a cationic surfactant, a zwitterionic surfactant and water to obtain a uniform transparent liquid, adding an aqueous solution of an electrolyte salt and counter ion to the uniform transparent liquid under stirring, and uniformly mixing to obtain the clean fracturing fluid. According to the present invention, the method has characteristics of simpleness and convenient operation, and the clean fracturing fluid system has characteristics of good viscoelasticity, strong sand-carrying ability, no residue, automatic gel breaking with water or oil, easy flowback, and low damage on stratum.