Electrolyte enhancement strategy becomes a promising route to improve flexible interdigitated miniaturized supercapacitors (IMSCs) performance due to the less mass loading of electrode materials on interdigitated electrodes. Herein, we develop a flexible polyvinyl alcohol/KOH (PVA/KOH) gel electrolyte with homogeneous BN-PDA (polydopamine modified boron nitride nanosheets) doping for enhancing energy storage of IMSCs, in which the conductivity is up to 112.1 mS cm−1 with excellent mechanical strength and heat stability. The ionicity of BN-PDA caused by electronegativity difference between B and N atoms significantly facilitates KOH transfer in PVA gel and diffusion in electrode diffuse layer by rapping-pairing effect. Furthermore, the different phase transition behavior of BN-PDA and PVA in water provides additional ions transmission pathways and effectively disperses external forces. With such excellent electrolytes, ultra-high energy density (14.7 μWh cm−2) at a high power density (420 μW cm−2) has been achieved for IMSCs. Moreover, the capacitance of IMSCs can always be maintained at a very high level during the long-term charge and discharge process. Our work suggests a feasible pathway to design inorganic fillers uniformly modified gel electrolyte with high conductivity and increased energy storage capacity of IMSCs as well as other flexible energy storage devices.