Two new crystal isomorphs consisting of complexes [(CH3CH2)(3)NH)](2)[MoO2(C14H6O4)(2)] (1) and [(CH3CH2)(3)NH)](2)[WO2(C14H6O4)(2)] (2) have been synthesized, respectively, and from which Mo-based flexible and durable nanopipes with diameters of 16 nm and lengths of hundreds of micrometers and W-based rigid and fragile nanotubules with ununiform diameters ranging from 30 to 100 nm and lengths in tens of micrometers have been prepared separately, which revealed that the change of the metal in the coordination center of the isomorphs can result in obvious variation to their nanostructures. The crystals both exhibited multilayered structures by the piling of lamellar repeating motifs through van der Waals forces, which are formed by the parallel alignment of 1D chains through hydrogen bonds, and the ID chains are assembled by complexes 1 and 2, respectively, through geometrical intercalation and pi-pi packing. However, under grinding and ultrasonication, crystal 1 disassembled uniformly into longer and narrower nanostrips, whereas crystal 2 were broken at random into shorter and wider nanoribbons; therefore, the two lamellar nanostructures curled into different cylindrical nanospecies. The differences caused by Mo and W are the following: the Mo complex prefers to assemble into more durable one-dimensional structures along Mo-O bonds than W isomorphs; since Mo-O bonds are weaker than Mo=O and W-O bonds, then the weakest Mo-O bonds can be supported by the adjacent molecules through intercalation and pi-pi packing, which resulted in that the linkages among the Mo complexes are stronger along the Mo-O direction and hence the longer Mo-based cylindrical structure. Moreover, the flexibility of Mo-based nanopipes and the rigidity of W-based nanotubules might be attributed to that Mo possesses a lower melting point than W; therefore, Mo is softer and W is harsher.