The invention discloses a non-contact low-passive intermodulation waveguide connection structure and a design method thereof. A periodic metal protruding body is designed at an outer wall of a waveguide and is used as a first connection part, a step waveguide with a matched size is designed at a tail end of another one waveguide and is used as a second connection part, the first connection part isembedded into the second connection part, and a non-contact waveguide connection structure is formed by mechanical connection. Appropriate electromagnetic forbidden band characteristic is obtained bycalculating parameters such as the size of the protruding body and internal distance of the connection structure, and suppression of electromagnetic leakage in a structural gap is achieved. In the non-contact low-passive intermodulation waveguide connection structure, the internal non-contact connection of the waveguide is achieved on the premise of no influence on electromagnetic transmission, contact non-linearity of traditional connection is eliminated, passive intermodulation effect is effectively prevented, and the requirement on material, processing and assembly technology is reduced; and meanwhile, the non-contact low-passive intermodulation waveguide connection structure has the advantages of wideband, compact structure, high tolerance and the like, and can be applied into variouslarge-power low-passive intermodulation microwave parts and test systems.