The invention discloses a magnetic flocculant which consists of a flocculant and a magnetic seed, wherein the weight ratio of the flocculant to the magnetic seed is (1-100):(1-5). The invention also discloses an application method of the magnetic flocculant, which comprises the following steps of: adding the magnetic flocculant into fermentation liquid rich in petroleum hydrocarbon degrading thalli according to a weight ratio of 0.1-0.5%; uniformly stirring, and standing in a magnetic field; and after the substance to be shaped is condensed, separating out the flocculating body rich in petroleum hydrocarbon degrading thalli by use of separation equipment. According to the magnetic flocculant and the application method thereof disclosed by the invention, by taking the fermentation engineering as a theoretical basis and combining the related theoretical knowledge of the magnetic separation science and the environmental engineering, the fermentation liquid thalli are recovered by use of an Fe3O4-containing magnetic flocculant to solve the problem in flocculation recovery of the fermentation liquid thalli in the traditional technology; and the magnetic flocculant and the application method thereof have the advantages that the flocculation recovery is fast, the magnetic flocculant brings little influence on the activity of the microorganism thalli, and the magnetic seed in the magnetic flocculant can be repeatedly recovered and used.