The invention relates to a chemical reactor based on a microwave separation field reconstruction technology. The chemical reactor comprises a second resonant cavity, a second microwave source, a firstmicrowave source, a to-be-treated sample, a test tube, a chemical reaction region and a first adjustable short-circuit surface; the first resonant cavity is inserted into one side of the second resonant cavity; a second coupling window is arranged in the first resonant cavity and close to the second resonant cavity; the second microwave source is arranged at one end of the first resonant cavity;a first coupling window is arranged in the second resonant cavity and close to the first resonant cavity; and the first microwave source is placed at one end of the second resonant cavity. According to the chemical reactor, through combination of the two orthogonal waveguide single-mode resonant cavities, the central positions of the two resonant cavities are respectively adjusted into an electricfield center and a magnetic field center; and through adjustment of the power of the two feed microwave sources, reconstruction of the microwave electric field and the magnetic field in the reactiontest tube is realized. The first coupling window and the first short-circuit surface form a first waveguide single-mode cavity resonator, and the second coupling window and a second short-circuit surface form a second waveguide single-mode cavity resonator.