The invention provides a preparation method and system of mixed gas for preparing an intermittent hypoxia animal model, mainly relates to the technical field of medical experiments. The system comprises a plurality of gas mixing devices for generating hypoxia gas, a cage box which is used for placing experimental animals and which is supplied with gas through the gas mixing devices, and a waste gas treatment device, wherein the waste gas treatment device is communicated with the cage box through a waste gas outlet pipe; the gas mixing devices are communicated with the cage box through a mixed gas inlet pipe, and the multiple gas mixing devices are connected to the mixed gas inlet pipe in parallel. Gas is mixed in the gas mixing devices in advance, then the mixed gas is input into the cage box for animal modeling, the gas mixing time can be shortened, animal modeling is more facilitated, the modeling efficiency is high, the success rate is high, meanwhile, batch animal modeling can be conducted, and the animal modeling efficiency is improved. The modeling time is shortened, the cost is reduced, the application range is wide, two airflow layouts are used for experimental animals with different body types and sizes, and the practicability is high.