Aqueous binary colloids of niobate and clay nanosheets, prepared by the exfoliation of their mother layered crystals, are unique colloidal systems characterized by the separation of niobate and clay nanosheet phases, where niobate nanosheets form liquid crystalline domains with the size of several tens of micrometers among isotropically dispersed clay nanosheets. The binary colloids show unusual photocatalytic reactions because of the spatial separation of photocatalytically active niobate and photochemically inert clay nanosheets. The present study shows structural conversion of the binary colloids with an external electric field, resulting in the onsite alignment of colloidal nanosheets to improve the photocatalytic performance of the system. The colloidal structure is reshaped by the growth of liquid crystalline domains of photocatalytic niobate nanosheets and by their electric alignment. Niobate nanosheets are assembled by the domain growth process and then aligned by AC voltage, although clay nanosheets do not respond to the electric field. Photocatalytic decomposition of the cationic rhodamine 6G dye, which is selectively adsorbed on clay nanosheets, is examined for the niobate-clay binary nanosheet colloids with or without domain growth and electric field. The fastest decomposition is observed for the electrically aligned colloid without the domain growth, whereas the sample with the domain growth and without the electric alignment shows the slowest decomposition. The results demonstrate the improvement of the photocatalytic performance by changing the colloidal structure, even though the sample composition is the same.