•The novel molecularly imprinted polymers (MIP) can be used in methanol–water media.•The specific ionic liquid (IL) was used as the functional monomer to prepare MIP.•ILs are easily designable.•A larger quantity of ILs are facile to be designed as functional monomer for MIP. A novel molecularly imprinted polymer (MIP) using the specific ionic liquid (i.e. 1-vinyl-3-carboxymethylimidazolium bromide, 1-vinyl-3-carboxyethylimidazolium bromide, 1-viny-3-carboxybutylimidazolium bromide, or 1-vinyl-3-carboxypentylimidazolium bromide) as functional monomer was prepared via precipitation polymerization, which can be used to selectively separate synephrine (SYN) from methanol–water media. Ionic liquids are facile to be designed with varying the cation or anion, which enables the specific ionic liquid to be effectively designed to be a functional monomer for the preparation of MIP. The MIP showed a good selectivity and high adsorption capacity for SYN in methanol–water media. The adsorption process could be described by the pseudo-first-order model, which meant that the adsorption kinetics described a diffusion-controlled process. The equilibrium data fitted well to the Freundlich model, indicating multilayer adsorption. Finally, the MIP were successfully applied as sorbent to selectively enrich and separate SYN from the extracts of Aurantii Fructus Immaturus with a relatively high recovery (80–90%).