Multi-material fused deposition modeling (FDM) is an advanced 3D printing technology that allows for the simultaneous use of multiple materials, each with its unique properties, in a single print job. It opens up new possibilities for creating intricate and functional 3D-printed multi-material objects. Multi-material FDM is particularly valuable in industries where multi-material capabilities are required to achieve the desired characteristics and performance in printed parts. Recently, FDM has been successfully used to fabricate multi-material gyroid structures, weaving together polylactic acid (PLA) and thermoplastic polyurethane (TPU) materials. The gyroid structure is a complex, three-dimensional, periodic minimal surface structure characterized by its intricate, intertwined network of interlocking channels. The cellular characteristic of gyroid structures makes it a prime candidate for lightweight and energy absorption applications. It was found that multi-material gyroid structures made with PLA and TPU materials can achieve intermediate mechanical properties, including elastic modulus, yield stress, and energy absorption, compared to single-material gyroids made with PLA or TPU. The mechanical properties of multi-material gyroid structures can be controlled by adjusting the relative density and the material ratio between TPU and PLA. However, the numerical simulation of gyroid structures can be challenging due to the intricate, complex, and highly porous nature of these structures, especially multi-material ones that need to consider the interaction between dissimilar materials. In this study, a numerical simulation model is developed that can predict nonlinear mechanical properties of multi-material gyroid structures using finite element analysis (FEA). Firstly, the gyroid is divided into two material regions and tetrahedral meshes are generated in each region. Two regions are assigned with the material properties of PLA and TPU, respectively. Then, the interaction constraints are added to the overlapped surfaces in two regions. The overlapped surfaces in the PLA region are set to master surfaces and the overlapped surfaces in the TPU region are set to slave surfaces. Finally, the displacement load is added to the top surface of the gyroid and the reaction forces on the bottom surface are summed up to calculate the total force. The force-displacement curves obtained from the simulation model are compared to the experimental results. It was found that by adjusting the material properties of PLA and TPU, the simulation model can accurately predict the mechanical behavior of multi-material gyroid structures. Although the material properties of PLA and TPU can be obtained from the tensile or compressive test, the simulation result of the gyroid can deviate from the experimental results. Because the materials in the gyroid structure are printed like thin curved walls. The asbuilt material properties can be different from the bulk material properties. The interfacial bonding between TPU and PLA can also affect the overall mechanical properties of multi-material gyroid structures.