The present invention discloses a method of controlling transmitting frequencies of microwave source, which includes the following steps of: a) collecting reflection frequencies of a load according to a pre-set sampling rate; b) calculating a change rate of the reflection frequencies collected in the step a; c) setting a reflection frequency threshold and a change rate threshold; d) comparing the reflection frequencies and the change rate with the reflection frequency threshold and the change rate threshold respectively; wherein if the reflection frequencies or the change rate is less than the threshold goes to step e or returns to the step a; e) sending control signals to the microwave source and tuning the transmitting frequencies; and f) returning to step a. The present invention also discloses a microwave transmission system thereof. The present invention can be applied in controlling microwave source consists of single magnetron tube or multiple magnetron tubes.