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. As‐obtained 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.