The morphology and intermolecular interaction are two of the most important factors in the design of highly efficient dye adsorbent in the industry. Millimeter-sized, bead-type, bio-based lignin/chitosan (Lig/CS) adsorbent was designed for the removal of Congo red (CR), based on the electrostatic attraction, π-π stacking, and hydrogen bonding, which were synthesized through the emulsification of the chitosan/lignin mixture followed by chemical cross-linking. The effects of the lignin/chitosan mass ratio, initial pH, temperature, concentration, and contact time on the adsorption were thoroughly investigated. The highest adsorption capacity (173 mg/g) was obtained for the 20 wt% Lig/CS beads, with a removal rate of 86.5%. To investigate the adsorption mechanism and recyclability, an evaluation of the kinetic model and an adsorption/desorption experiment were conducted. The adsorption of CR on Lig/CS beads followed the type 1 pseudo-second-order model, and the removal rate for CR was still above 90% at five cycles.