We investigate the emission of active galactic nucleus (AGN) dusty tori in infrared domain. Following theoretical predictions derived from hydrodynamical simulations, we model the dusty torus as a 3D two-phase medium with high-density clumps and low-density medium filling the space between the clumps. Spectral energy distributions (SEDs) and images of the torus at different wavelengths are obtained using the 3D Monte Carlo radiative transfer code skirt. Our approach of generating clumpy structure allows us to model the tori with single clumps, complex structures of merged clumps or interconnected sponge-like structure. A corresponding set of clumps-only models and models with smooth dust distribution is calculated for comparison. We found that dust distribution, optical depth, clump size and their actual arrangement in the innermost region all have an impact on the shape of near- and mid-infrared SED. The 10-μm silicate feature can be suppressed for some parameters, but models with smooth dust distribution are also able to produce a wide range of silicate feature strength. Finally, we find that having the dust distributed in a two-phase medium might offer a natural solution to the lack of emission in near-infrared, compared to observed data, which affects clumpy models currently available in the literature.