The present invention provides a method of manufacturing a waveguide assembly and a structure thereof, wherein the manufacturing method comprises the steps of: providing at least two waveguide units and combining the waveguide units, wherein each waveguide unit has at least one bonding portion formed at a position where each two said waveguide units are combined; and at least one adhesive is applied to the bonding portion to combine the waveguide units into the waveguide assembly. With the practice of the present invention, many advanced functions such as rapid design, rapid manufacture, rapid verification and cost reduction can be achieved.