The invention discloses a multi-crosslinking polyurethane elastomer and a preparation method thereof, and relates to the field of polymer materials. The multi-crosslinking polyurethane elastomer is synthesized from a polyhydroxy macromolecular crosslinking agent, polyisocyanate and polyol. A main chain of the polyhydroxy macromolecular crosslinking agent is an acrylate structural unit, and side arms thereof contain a large number of hydroxyl groups, so that the crosslinking density of a polyurethane material can be significantly increased; moreover, the multi-crosslinking polyurethane elastomer is good in compatibility between various components, free of a phase separation phenomenon, relatively high in tensile strength and the elongation at break and excellent in mechanical properties. The preparation method of the multi-crosslinking polyurethane elastomer is simple in operation process and low in equipment requirement, and is suitable for large-scale industrial production.