The invention relates to an automatic detection device of a magnetron and an operation method thereof. The automatic detection device of the magnetron comprises power measuring equipment, a frequency meter and an integrated display, wherein the power measuring equipment is used for detecting the average power Po of the magnetron, the frequency meter is used for detecting the frequency fo of the magnetron, and the integrated display is used for detecting the electron emission frequency eta of the magnetron. The operation method comprises the following steps of 1, putting the magnetron on a conveying belt; 2, detecting the magnetron, and after detection, enabling the system to automatically record the detection data, wherein the recorded data comprises Po, Ebm and Ib; 3, calculating the electron emission efficiency eta of the magnetron, namely eta=(Po/(Ebm*Ib))*100%; and 4, when the electron emission efficiency eta of the magnetron is greater than or equal to 72%, and the frequency fo of the magnetron detected by the frequency meter is 2450MHz to 2470MHz, judging that the magnetron is qualified. The automatic detection device and the operation method have the advantages that the structure is simple and reasonable, the operation is flexible, the working efficiency is high, and the accuracy is high.