In virtual cathode oscillator (VIRCATOR) research, multi-frequency and multi-mode microwaves are coupled out and propagate along a waveguide. Identifying the microwave propagating modes has become a priority work for further research on microwave radiation physical mechanisms. Generally, an antenna matrix at the end of an open waveguide, which can shape the radiated microwave power distribution, is used to identify the microwave propagating modes [1-2]. Actual microwave radiation mechanisms in a VIRCATOR are complicated. Multi propagating modes and multifrequency microwaves coexist simultaneously, which challenges the antenna matrix method. In this paper, based on microwave propagating theory in a waveguide, a new method is proposed to identify multi-frequency and multi-mode microwaves, which is partially justified by the experimental data at Texas Tech University.