Nanocrystals of three-dimensional pillared-layer type porous coordination polymers, [Zn-2(ndc)(2)(dabco)](n), were fabricated by microwave-assisted coordination modulation, and its morphology was controlled by changing the modulator concentration. Adsorption measurement supported that the crystallinity and intrinsic porosity were maintained even for nanosized crystals, comparable to the corresponding micrometer-sized bulk powder crystals.