Herein, a novel and high-performance adsorbent, polyaniline-sodium alginate (PANI-SA) hydrogel microspheres were prepared via ion cross-linking technique for adsorption and removing methylene blue (MB) dye from wastewater. The processes involved synthesizing polyaniline (PANI) with macromolecular skeleton and doping it into sodium alginate (SA) to prepare hydrogel microspheres with high specific surface area, abundant functional groups, and excellent adsorption properties. The surface morphology, crystallinity, functional groups, thermal stability, pore size distribution, and specific surface area of PANI-SA hydrogel microspheres and their components were determined by SEM, XRD, FTIR, TGA, and BET. Various parameters, including polyaniline doped concentration, solution pH, initial dye concentration, adsorption time, and temperature were systematically investigated to understand their impact on the adsorption properties of PANI-SA. The results revealed a synergistic effect between PANI and SA, with PANI-SA exhibiting exceptional efficacy (1060.78 mg/g) in removing MB from aqueous solutions. The kinetics and isotherm adsorption behaviors were aptly described by the pseudofirst-order kinetic and the Langmuir isotherm models, respectively. Thermodynamic analyses confirmed the spontaneous and exothermic nature of adsorption. Furthermore, the PANI-SA hydrogel microspheres demonstrated excellent reusability, maintaining high adsorption capacity after 5 recycling rounds. Electrostatic interactions and hydrogen bond were found to be the primary mechanisms driving the adsorption process. This study not only contributes to the development of efficient and eco-friendly adsorption materials for dye wastewater treatment but also provides insights into the design and optimization of hydrogel adsorbents.