Acanthopanax senticosus extract with excessive standard of Pb, Cd, Hg, and Cu was used as the research object, and the alkyl thiourea functionalised silica was used as a new heavy metal removal scavenger. The heavy metal removal process was optimised by orthogonal experiment with dynamic and static adsorption modes. Meanwhile, the content of Acanthopanax B and Acanthopanax E, the solid content, and the HPLC fingerprint similarity were used as quality monitoring indicators of Acanthopanax senticosus heavy metal removal before and after. Then, the technical adaptability of heavy metal removal by alkyl thiourea functionalised silica was evaluated. Under the optimal dynamic adsorption conditions, the average removal rates of Pb, Cd, Hg, and Cu were 91.64%, 93.04%, 81.77%, and 83.11%, respectively. Under the optimal static adsorption conditions, the average removal rates of Pb, Cd, Hg, and Cu were 82.22%, 89.95%, 81.26%, and 82.97%, respectively. During Acanthopanax senticosus extract heavy metal removal before and after, the change percentage of Acanthopanax B and Acanthopanax E was less than 2.00%, the solid content loss rate was only 0.18%, and the fingerprint similarity was over 99.9%. The method can be used to satisfy the high efficiency of selective removal of harmful elements in Acanthopanax senticosus extract and the effective composition of almost no effect; the method is simple and easy, so it can be recommended for pretreatment of heavy metals in Traditional Chinese Medicine extracts, and this way provides a new thought and research technique to decrease the contents of heavy metals.