Abstract Most metal-organic frameworks (MOFs) hardly maintain their physical and chemical properties after exposure to acidic, neutral, or alkaline aqueous solutions, resulting in insufficient stability, therefore limiting their applications. Thus, the design and synthesis of stable size/morphology-controlled MOF nanocrystals is critical but challenging. In this study, dual-ligand and hard-soft-acid-base strategies were used to fabricate a variety of 3D pillared-layer Ni(thiophene-2,5-dicarboxylate)(4,4′-bipyridine)n MOF nanocrystals (1D nanofibers, 2D nanosheets and 3D aggregates) with controllable morphology by varying the concentration of 4,4′-bipyridine and thus controlling the crystal growth direction. Owing to the shorter ion diffusion length, enhanced electron/ion transfer and strong interactions between thiophene-2,5-dicarboxylate and 4,4′-bipyridine, the 2D nanosheets showed much larger specific capacitance than 1D nanofibers and 3D aggregates. A single device with an output voltage as high as 3.0 V and exceptional cycling performance (95% of retention after 5000 cycles at 3 mA cm–2) was realized by configuring two aqueous asymmetric supercapacitive devices in series. The excellent cycling property and charge–discharge mechanism are consistent with the hard-soft-acid-base theory. A unique method combines dual-ligand with hard-soft-acid-base strategies to achieve the morphology-controlled formation of the 3D pillared-layer MOF nanocrystals, which can effectively promote the electrochemical cyclic stability.