Adsorption and purification of biological molecules with pharmacological functions over advanced adsorption materials are always a concern. In this work, manganese oxide octahedral molecular sieve (OMS-2)-modified ZrO2 nanocomposites (ZrO2-OMS-2) were fabricated and their adsorption performance towards rutin from aqueous solution was investigated. Asobtained nanocomposites were fully characterized by N2 adsorption/desorption isothermal, ICP-AES, XRD, SEM and TEM, which indicates that OMS-2-modification significantly promoted the textural properties of the nanocomposites. 10 mol% Mn amount for ZrO2-OMS-2 showed the optimal adsorption capacity for rutin due to the enhanced specific surface aera (104 m2/g) and better ZrO2 dispersion. The adsorption rate of 85% was realized over 10 mg of the optimal adsorbent and the desorption rate could reach nearly 100% in 0.2% TFA/methanol solution. Moreover, the adsorbent could be reused for at least 3 times. The adsorption behavior was fitted the pseudo-second-order model and Freundlich model. Kinetic and thermodynamic studies suggested that an endothermic chemosorption from Lewis acid-base paring on the surface of ZrO2-OMS-2 was responsible for the good adsorption. This work shows the positive effect of manganese oxide-modification for ZrO2 during adsorption process and the potential of ZrO2-based nanocomposites being adsorbents.