3D printable multi-material honeycombs have attracted increasing interest recently due to the improved elastic moduli, buckling and energy absorption properties. This paper proposes an analytical homogenization for the equivalent in-plane elastic moduli (EIEM) of multi-material honeycombs. First, the axial and bending stiffness of a cantilever beam consist of three sections made of different materials is formulated. Then based on unit cell method and cantilever beam model, the closed-form expressions of EIEM are proposed by fully considering the deformations of both joints and cell walls with arbitrary stiffness, which are sufficiently general to be applied to hexagonal, auxetic and rectangular multi-material honeycombs and validated very well by numerical simulations and experiments. Furthermore, the effects of geometric and material distribution ratios on EIEM are discussed. The results show that the geometric and material distribution ratios of inclined cell wall have a significant effect on all five EIEM while that of vertical cell wall shows a significant effect on shear modulus but only a slight effect on y- direction elastic moduli. Compared with single-material honeycombs, changing joint stiffness has a significant effect on the equivalent Young’s moduli and shear modulus but a slight effect on Poisson’s ratios.