Here we report a simple and versatile strategy for the in situ fabrication of nanogel-containing smart membranes in microchannels of microchips. The fabrication approach is demonstrated by the in situ formation of a chitosan membrane containing poly(N-isopropylacrylamide) (PNIPAM) nanogels in a microchannel of a microchip. The PNIPAM nanogels, that allow temperature- and ethanol-responsive swelling-shrinking volume transitions, serve as smart nanovalves for controlling the diffusional permeability of solutes across the membrane. Such self-regulation of the membrane permeability is investigated by using fluorescein isothiocyanate (FITC) as a tracer molecule. This approach provides a promising strategy for the in situ fabrication of versatile nanogel-containing smart membranes within microchips via simply changing the functional nanogels for developing micro-scale detectors, sensors, separators and controlled release systems.