The invention discloses a pre-reactor for organic waste water difficult to degrade and an application method, which belongs to the field of environmental engineering. For the problem that the organicmatter polluted waste water is low in biodegradability, the invention provides a pre-reactor for the organic waste water difficult to degrade and an operation method. The pre-reactor comprises a container, a microwave transmitter, a power apparatus and stirring blades, wherein the microwave transmitter is arranged on a center position of the container, a root portion of each stirring blade is connected with the microwave transmitter, and each stirring blade is fixedly provided with a catalyst; and the power apparatus drives the microwave transmitter to rotate. The biodegradability of the wastewater treated by the pre-reactor disclosed by the invention is significantly improved, and the waste water can directly enter a secondary biochemical treatment process.