Dye pollution is a serious issue in current environment protection, and bio-based adsorbents have been receiving much attention in wastewater treatment, due to their low cost, renewable, and environmentally friendly characteristics. Bio-based sodium alginate/lignin composite (SA/Lig) hydrogel beads were fabricated by a facile cross-linking with calcium ion and used for the removal of methylene blue (MB). The obtained SA/Lig microbeads were characterized with SEM, FTIR, and TG, and the effect of lignin content, pH, and temperature on the MB adsorption was investigated. The results indicated that the introduction of aromatic lignin can not only enhance thermal stability but also can improve the adsorption performance. Under optimal conditions, the maximum adsorption capacity (254.3 mg/g) was obtained for the SA/Lig-20% beads, with a removal efficiency of 84.8%. The adsorption process for MB is endothermic, and the rate-limiting step is chemical adsorption. The removal efficiency is higher than 90% after five cycles, revealing that the prepared beads show good regeneration ability.