β-cyclodextrin modified Schwertmannite has been successfully biosynthesized by Acidithiobacillus ferrooxidans in this study. Three main parts in this experiment are as follows: characterisation, adsorption measurements and mechanisms exploration. The stability of micro-sphere structure was reduced with β-cyclodextrin modification, while the functional groups was enhanced by β-cyclodextrin. In addition, the adsorption capabilities of Schwertmannite, formed in oversaturated β-cyclodextrin, were improved by 20.66% for Cu(II) and 14.82% for Cr(VI) respectively. However, the improvement of Cu(II) was associated with decreasing adsorption rates while that of Cr(VI) was companied with increasing rates. Both metal adsorptions can be roughly regarded as two adsorption phases: surface adsorption and the migration of metal ion in channels inside Schwertmannite. In binary metal solutions with high concentration, modified Schwertmannite materials showed distinct affinity to Cr(VI) instead of Cu(II). In terms of mechanisms, Cu(II) adsorption depended on the H+ exchange and Cr(VI) relied on the ligand exchange, such as SO42−.