Compared with seismic reflection wave, the seismic scattered wave has better ability to descript the formation details, therefore, we carried out the exploratory study on the separation method of seismic scattered wave and reflection wave. The paper analyzed the wave field characteristic difference and similarity between the reflection wave and the scattered wave, and put forward a new idea and scheme based on the diffusion filter of thermal conductivity equation to achieve the multi-scale separation of the reflection wave energy and the scattered wave energy according to the basic thermal conductivity theory. Taking the pre-stack migration data of practical 3D seismic project as examples, this paper carried out wave field separation processing of the reflection wave and scattered wave. The result shows that the proposed method can relatively separate the reflection wave and scattered wave, and they can respectively reflect the macroscopic and microscopic features of formation. The computation results are accurate and reliable, in which the S/N of the scattered wave energy is relatively poor, but it can reflect the fracture and heterogeneous geologic body edge, and it is more effective to descript the microscopic detail features covered by conventional seismic reflection wave energy. Therefore, the proposed method can provide an important reference value for practical seismic data processing.