Some challenges still hinder the advancement of hydrogel electrolytes, such as low ionic conductivity and restricted flexibility, which obstacle the effective integration of supercapacitors for flexible wearable devices. We developed an amphoteric hydrogel electrolyte with a highly ionic conductivity of 46.64 mS·cm−1, 927.32% of tensile strain and compressive strain to 85% in ambient air. Through lignin sulfomethylation and chitosan quaternization, abundant charge groups were introduced to the structure of hydrogel electrolyte to achieve charge modification. These charged groups not only promoted the dissociation of KOH, but also formed ion transport channels to enhance the migration of K+ and OH–. Note that the hydrogel also had significant antibacterial activity, enhancing its practical applicability. Moreover, the flexible supercapacitor constructed with this hydrogel electrolyte showed excellent capacitive performance, achieving a notable specific capacitance of 192.6 F·g−1 and a high energy density of 45.2 Wh·kg−1 under a current density of 0.5 A·g−1. In addition, the flexible supercapacitor also demonstrated remarkable rate performance and cycle stability, which maintained nearly constant coulombic efficiency (99.7%) and retaining 86.1% of capacitance retention after 10,000 charge–discharge cycles. Moreover, the flexible supercapacitor maintained stability under bend and load conditions, showing good deformation adaptability.