The invention discloses a magnetic encoder based on double synchronous rotation coordinate systems. The magnetic encoder based on the double synchronous rotation coordinate systems comprises a magneto-electricity signal generator, a signal conditioner, a signal acquisition module and a signal processing unit, wherein the signal processing unit is composed of a forward-direction Parker converter, a reverse-direction Parker converter, a forward-direction decoupling device, a reverse-direction coupling device, low-pass filters and a motion information solver, and is used for carrying out coordinate transformation, decoupling operation, filtering processing and motion information calculation on digital electrical signals input by the signal acquisition module. The signal processing unit which uses the double synchronous coordinate transformation mode carries out coordinate transformation on positive sequence components and negative sequence components of fundamental waves in magneto-electricity signals, and resolves the positive sequence components and the negative sequence components of the fundamental waves into components in a positive sequence dq coordinate system and components in a negative sequence dq coordinate system, calculation of motion information is achieved through a decoupling network and the filtering link, signal distortion components generated due to device difference, installation errors and the like can be eliminated through the decoupling devices and the low-pass filters, and thus calculation accuracy and the anti-interference capacity of the magnetic encoder are greatly improved.