The utilization of acid as a synthesis assistant provides an effective means to regulate the structure of hydrogels, thereby simplifying the design and preparation process of multifunctional hydrogels. However, there remains a dearth of discourse concerning the utilization of this convenient acid-mediated strategy, which possesses the potential to directly govern molecular interactions within gel networks for rational structure and property design. Herein, we describe the preparation of flexible dual-network conductive hydrogels using polyacrylamide (PAM) and sodium alginate (SA) as substrates, driven by the strategy of acid-mediated (HCI, H2SO4, and H2C2O4) in detail for the first time. Especially, the structure-activity relationship of hydrogels was elucidated through a comparative analysis of molecular dynamics (MD) simulations and empirical properties, thereby enhancing the understanding of this field. Furthermore, extensive investigations have been conducted to explore the distinct impacts of acid ions and concentrations. The acid-mediated method exhibits superior versatility and operability compared to the filler modification method, thereby enabling a more convenient acquisition of conductive and robust hydrogels suitable for flexible capacitors and wearable sensors. Consequently, this study presents a straightforward, efficient, and cost-effective universal strategy for targeted functional hydrogel design.