The invention discloses an E-band duplexer with transmission zero. The E-band duplexer comprises a public port and two input/output ports, wherein six resonant cavities are formed between the public port and each of the two input/output ports; the positions of the resonant cavities are staggered and arranged in a snake-shaped line manner; a boss is arranged on the resonant cavity on the outermost side; a 90-degree turning structure is arranged at each of the input/output ports; a butterfly-shaped structure for turning the polarization direction by 90 degrees is arranged at the public port. According to the E-band duplexer with the transmission zero, the problem of leakage caused by a too thin isolation wall is avoided by adopting a similarly snake-shaped line mode. Due to the butterfly-shaped structure of the public port, the signal polarization direction is turned by 90 degrees, so that a 90-degree included angle exists between the public port and each of the input/output ports of the duplexer. The input/output ports are of waveguide 90-degree turning structures, so that the problem of difficulty in machining the waveguide 90-degree turning structures in a high frequency band is solved. The E-band duplexer has the advantages of simple structure, convenience for machining, better performance and the like.