The invention provides a two-component polyurethane sealant for insulating glass and a preparation method thereof. The sealant is prepared from a component A and a component B, wherein the component Acomprises the following components in parts by weight: 20-40 parts of hydroxyl terminated liquid polybutadiene, 10-30 parts of plasticizer, 10-30 parts of filler, 2-50 parts of thixotropic agent, 0.01-2 parts of chain extender, 0.01-2 parts of catalyst a, 0.2-2 parts of water absorbing agent, 0.01-0.5 part of UV stabilizer and 0.01-0.5 part of antioxidant; the component B comprises the followingcomponents in parts by weight: 20-50 parts of isocyanate, 10-30 parts of isocyanate polymer, 10-30 parts of plasticizer, 0-40 parts of filler, 2-10 parts of thixotropic agent, 5-15 parts of silane coupling agent and 0.01 to 2 parts of catalyst b, wherein the isocyanate polymer is prepared from hydroxyl terminated liquid polybutadiene and diisocyanate through reaction. The sealant has good water tightness and airtightness and has good adhesion to a substrate.