This study reports the design and fabrication of a novel hybrid microcapsule adsorbent, denoted as Pillar[6]-Sp, via the covalent immobilization of pillar[6]arene macrocycles onto modified sporopollenin (Sp) for the efficient removal of Rhodamine B (RhB) from aqueous media. The adsorbent was synthesized via sequential functionalization of natural Sp with APTMS and alkyne moieties, followed by covalent coupling with an azide-functionalized pillar[6]arene derivative. The successful construction and structural integrity of the Pillar[6]-Sp microcapsule adsorbent biopolymer were confirmed by scanning electron microscopy (SEM), Fourier transform infrared (FT-IR), and energy dispersive x-ray (EDX) analyses. Batch adsorption experiments were systematically conducted to investigate the effects of pH, contact time, adsorbent dosage, and temperature on the removal performance. The adsorption process reached equilibrium within 90 min at an optimal pH of 9.0. The maximum Langmuir adsorption capacity was determined to be 37.74 mg g−1 at 328 K. Equilibrium data were best fitted by the Langmuir isotherm model, while the adsorption kinetics followed a pseudo-second-order (PSO) model, indicating a monolayer chemisorption mechanism. Thermodynamic parameters (ΔG°, ΔH°, and ΔS°) revealed that the adsorption process is spontaneous, endothermic, and entropy-driven. The enhanced adsorption performance of Pillar[6]-Sp is attributed to the synergistic contribution of supramolecular host–guest interactions, π–π stacking, and electrostatic attractions. Furthermore, the adsorbent demonstrated excellent reusability, maintaining high removal efficiency over six consecutive cycles. These findings highlight the potential of Pillar[6]-Sp as a sustainable, efficient, and environmentally friendly adsorbent for the treatment of dye-contaminated wastewater.