The invention discloses a multifunctional phosphite water-soluble fertilizer and a preparation method thereof, and relates to the technical field of agricultural fertilizers. The phosphite multifunctional water-soluble fertilizer comprises phosphite, activated humic acid, phosphate and nutrient elements, the phosphate is composed of N, P2O5 and K2O, the nutrient elements are one or more of B, Mn, Cu, Zn, Mo and Fe which are mixed according to any proportion, the mass ratio of phosphorous acid phosphorus to phosphoric acid phosphorus in the phosphite (in terms of P2O5) is 1: (0.3-1.2), and the concentration of the activated humic acid is 20-80 g / L. According to the present invention, the phosphite and the activated mineral source humic acid are adopted as the basis, the antibacterial, nutritional and multifunctional water-soluble fertilizer with the macro-nutrition element and the micro-nutrition element is matched, the growth and development requirements of various crops are met, the chemical activity and the biological activity are improved by activating the mineral source humic acid, and the nutrition, the antibacterial property and the physiological regulation are integrated.