This paper presents the method of moments based on electric field integral equation which is capable of solving three-dimensional metallic waveguide problem with no use of another method. Metals are treated as perfectly electric conductor. The integral equation is derived in detail. In order to validate the proposed method, the numerical results are compared with those in a published paper. Three types of waveguide are considered: step discontinuity waveguide, symmetrical resonant iris waveguide, and unsymmetrical resonant iris waveguide. The numerical results are also verified by the law of conservation of energy.