The invention discloses a method for carrying out high precision synchronous decoding processing by acquiring data of an electronic mutual inductor using Manchester encoding, which is mainly used in an intelligent or digital transformer station and belongs to the field of a power system and automation thereof. The method comprises the following steps: while decoding an IEC60044-7/8 message by using a programmable logic controller, outputting a data frame synchronizing pulse signal; carrying out interpolation on the data by using the measurement data frame synchronizing pulse signal and a clock signal; and simultaneously generating synchronous sampled data and asynchronous sampled data. The invention comprehensively utilizes the advantages of the pulse synchronization method and the interpolation method, solves the problem of data and time synchronization in the electronic mutual inductor in an intelligent or digital transformer station, and does not relate to bigger synchronous acquisition technical innovation on the electronic mutual inductor.