Surface modification of niobate nanosheets in a double-Y-type microchannel was achieved for the first time using parallel flows of an aqueous dispersion of nanosheets derived from ion-exchangeable layered perovskite via delamination with a tetrabutylammonium hydroxide aqueous solution and a cyclohexane solution of oleyl phosphate. The surface modification was essentially completed within 4.6 s, and spectroscopic characterization (IR, solid-state 13C and 31P NMR) demonstrated the successful surface modification. The surface modification using a biphasic system in a vial using the same liquids required more than 4 h, indicating the extremely high efficiency of surface modification in the microchannel.