We report a metal ion-modulated effective strategy to achieve different metal-organic framework (MOF) micro/nanostructures using different metal precursors like CoCl2 center dot 6H2O, CoCl2 center dot 6H2O and NiCl2 center dot 6H2O, and NiCl2 center dot 6H2O with pyridine-3,5-dicarboxylate (3,5-pdc). The structural characterizations confirm that different morphological structures, hollow microsphere, hierarchical nanoflower, and solid nanosphere are for Co-(3,5-pdc), Co0.19Ni0.81-(3,5-pdc), and Ni-(3,5-pdc), respectively. These different MOF micro/nanostructures correlate with the coordination ability of Co and Ni with 3,5-pdc. Benefitting from the synergistic effect of the alloying metal nodes of Co and Ni producing rapid and rich redox reactions and the hierarchical nanoflower with higher surface area enabling excellent ion kinetics, the Co0.19Ni0.81-(3,5-pdc) exhibits higher specific capacitance of 515 F g-1/273 C g-1at 0.5 A g-1 than that of Ni-(3,5-pdc) (290 F g-1/153.7 C g-1) and Co-(3,5-pdc) (132 F g-1/67 C g-1), good rate capability and cycling stability. Moreover, the asymmetric supercapacitor device (Co0.19Ni0.81-(3,5-pdc)//AC) assembled from Co0.19Ni0.81-(3,5-pdc) and activated carbon (AC) achieves a maximum energy density of 42.6 Wh kg-1 at a power density of 277.3 W kg-1.