The strategy of crystal structure transformation tunes the electrochemical properties favoring the energy storage performance of the electrode material. Herein, we prepared SnWO4 nanoflakes through Sn incorporation into the tungsten oxide matrix by a single-step wet chemical method. The crystal structure tuning occurs from the orthorhombic structure of hydrated tungsten oxide (WO3·H2O, i.e., HWO) to the hexagonal (SnWO4, i.e., SWO) structure. Simultaneously, the morphology tailoring from nanodisks of HWO to nanoflakes of SWO is realized as a result of the Sn ion exchange mechanism. Further, the electrochemical supercapacitor of SWO nanoflakes demonstrates almost 2-fold enhancement in the specific capacitance of 622 F g–1 at 0.5 A g–1 over HWO nanodisks (255 F g–1). Moreover, the asymmetric supercapacitor (ASC) of SWO//activated carbon (AC) exhibits the specific capacitance of 50 F g–1 at 1 A g–1, with the maximum energy density and power density of 18 Wh kg–1 and 7000 W kg–1, respectively. Furthermore, superior performance of the aqueous zinc-ion battery (AZIB) demonstrates the specific capacity of 75 mA h g–1 at 0.3 A g–1 along with 106% stability and 101% coulombic efficiency after 70 cycles. The improved performance of SWO nanoflakes in the pseudocapacitor and AZIB is attributed to crystal structure tuning, increasing conductivity, enhanced surface area, and Sn redox sites. Therefore, the SWO nanoflakes are favorable cathode materials for commercial energy storage devices.