The invention belongs to the technical field of polyurethane modification and particularly relates to a high-water-tolerance transparent prepolymer and a preparation method thereof. The high-water-tolerance transparent prepolymer is prepared from the following raw materials in parts by weight: 100-200 parts of polyether polyol A, 80-160 parts of polyether polyol B, 2-15 parts of isocyanate, 10-40 parts of a chain extender, 0.3-0.8 part of a catalyst and 35-50 parts of an organic solvent. By adding aliphatic diisocyanate into a formula, the prepared high-water-tolerance transparent prepolymer has good stability, is unlikely to discolor and can meet the requirements of clients on tones and transparency through a compounding action of the components; by modifying, the water tolerance of the high-water-tolerance transparent prepolymer is improved, the high-water-tolerance transparent prepolymer has excellent comprehensive performance, is safe and environmentally friendly and can be applied to the fields of hydrolysis-resistant surface paint, protective sleeves and outdoor decoration; and the preparation method is simple, feasible and easy to implement.