The invention discloses a microwave synthesis method of 1,3-bis[2-(3,4-epoxycyclohexyl)ethyl]tetramethyldisiloxane. Including: (1) Under the protection of inert gas, sequentially add tetramethyldisiloxane, organic solvent, 4-vinyl-1,2-epoxycyclohexene into the reaction flask and stir, and then add the supported Pt / Y molecular sieve catalyst, finally add absolute ethanol, continue to stir to obtain a suspension; (2) move the suspension into a microwave synthesis reactor for reaction, after the reaction, the reaction solution is decompressed to remove solvents and low boilers, and then centrifuged , to give 1,3-bis[2-(3,4-epoxycyclohexyl)ethyl]tetramethyldisiloxane. The invention has mild reaction conditions, short reaction time, high conversion rate of raw material active hydrogen, excellent activity and stability of the catalyst, recyclable reuse, reduced cost, high yield of the prepared target product, and good industrialization prospect.