The radiation-induced segregation is one of the major concerns for nuclear materials, as it can damage the service performance of the material. Eutectic high entropy alloy (HEA) multilayer is considered a potential nuclear material for improving the irradiation tolerance of materials, due to its outstanding irradiation tolerance and mechanical properties. Abundant heterogeneous interfaces in eutectic HEA multilayer can interact with irradiation-induced vacancies, thus resulting in changes in the behavior of atomic diffusion and segregation. In the current work, to explore the effects of the heterogeneous interfacial structure on atomic diffusion and segregation, we have investigated the evolution of the elemental distribution in FCC/BCC HEA multilayers with coherent and semicoherent interfaces under vacancy flow in detail. It is found that the segregation and atomic diffusion behaviors of eutectic HEA multilayer are sensitive to the heterogeneous interfacial structure. The semicoherent interface promotes the interface diffusion and interface segregation due to the vacancy annihilation at interface and the intrinsic excess volume of interface. Whereas, the coherent interface is benifcial to the intragranular diffusion because it is transparent for the diffusion of vacancy.