Inorganic layered materials can be converted to colloidal liquid crystals through exfoliation into inorganic nanosheets, and binary nanosheet colloids exhibit rich phase behavior characterized by multiphase coexistence. In particular, niobate-clay binary nanosheet colloids are characterized by phase separation at a mesoscopic (∼several tens of micrometers) scale whereas they are apparently homogeneous at a macroscopic scale. Although the mesoscopic structure of the niobate-clay binary colloid is advantageous to realize unusual photochemical functions, the structure itself has not been clearly demonstrated in real space. The present study investigated the structure of niobate-clay binary nanosheet colloids in detail. Four clay nanosheets (hectorite, saponite, fluorohectorite, and tetrasilisic mica) with different lateral sizes were compared. Small-angle X-ray scattering (SAXS) indicated lamellar ordering of niobate nanosheets in the binary colloid. The basal spacing of the lamellar phase was reduced by increasing the concentration of clay nanosheets, indicating the compression of the liquid crystalline niobate phase by the isotropic clay phase. Scattering and fluorescence microscope observations using confocal laser scanning microscopy (CLSM) demonstrated the phase separation of niobate and clay nanosheets in real space. Niobate nanosheets assembled into domains of several tens of micrometers whereas clay nanosheets were located in voids between the niobate domains. The results clearly confirmed the spatial separation of two nanosheets and the phase separation at a mesoscopic scale. Distribution of clay nanosheets is dependent on the employed clay nanosheets; the nanosheets with large lateral length are more localized or assembled. This is in harmony with larger basal spacings of niobate lamellar phase for large clay particles. Although three-dimensional compression of the niobate phase by the coexisting clay phase was observed at low clay concentrations, the basal spacing of niobate phase was almost constant irrespective of niobate concentrations at high clay concentrations, which was ascribed to competition of compression by clay phase and restoring of the niobate phase.