Recently, shikimic acid (SA) has aroused great concern as the starting raw material for the synthesis of antiviral drug (Tamiflu) against the spread of influenza virus in the body. In this work, magnetic chitosan composite modified with boric acid and its application in SA recognition and separation was described. Chitosan (CT) with plenty of hydroxyl and amino groups was first coated on the surface of magnetic core Fe3O4, then carboxylic groups were grafted to the surface of Fe3O4@CT via anhydride modification, followed by the introduction of 3‐aminophenylboronic acid (APBA). The uniform morphology and composition analysis of the adsorbent (Fe3O4@CT‐COOH‐BA) were characterized by FT‐IR, XRD, XPS, SEM, TEM and UV–visible spectroscopy. The adsorption capacity of as‐prepared material was explored in detail by batch mode experiments. The adsorption kinetics fitted well with a pseudo‐second order model, and the adsorption isotherms was well described by the Langmuir model with a maximum adsorption capacity of 23.8 mg g−1 at 25 °C. Solution pH plays a crucial role in adsorption process and the optimized pH was 8.0. In addition, Fe3O4@CT‐COOH‐BA could be easily reused through an external magnet and the adsorption capacity reduced by only 4% after five adsorption–desorption cycles. These results prove that boric acid modified magnetic chitosan composite is an effective and practical adsorbent for specific recognition and selective adsorption of cis‐diol‐containing compounds.