The invention discloses hydrophobic heat-resistant silicone modified polyester resin and a preparation method thereof. Specifically, the hydrophobic heat-resistant silicone modified polyester resin is prepared from the following components in parts by weight: 3-8 parts of dihydric alcohol, 100-120 parts of triatomic alcohol, 60-120 parts of diacid, 100-250 parts of silicone intermediate, 0.5-1 part of catalyst, 5-10 parts of water-carrying agent and 160-240 parts of organic solvent, wherein the weight-average molecular weight of the silicone intermediate is 800-2000, and the silicone intermediate contains 3-20% of hydroxyl and 2.5-15% of methoxyl or ethoxy group. The hydrophobic heat-resistant silicone modified polyester resin has excellent hydrophobic property, heat resistance, oxidative resistance and anti-yellowing performance, and also has low surface energy, good pollution resistance, metal adhesive force and mechanical energy. The technical process of the preparation method is simple in operation, and repeatability is good.