(Objectives) A novel method was developed for extracting and determining flavonoids from marine mangrove medicinal plants. This approach utilizes surface molecular imprinting to increase selectivity. Graphene oxide doped with a SiO2–Ag2O dual core structure served as a scaffold for synthesizing multilayer surface-imprinted polymers. The surface of the SiO2-Ag2O@GO composite was modified through self-polymerization. (Methods) Acacetin molecularly imprinted polymers (AMIPs) were created via surface-initiated precipitation polymerization with acacetin as the template. These AMIPs were synthesized and characterized via ultraviolet (UV) spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM), X-ray diffraction (XRD), and transmission electron microscopy (TEM). Recycling experiments demonstrated the stability of the AMIPs. Analysis of the adsorption mechanism via the Langmuir and Freundlich models indicated that the Langmuir model was more suitable for predicting AMIPs. (Results) Scatchard plots showing two different binding sites of AMIPs for acacetin adsorption at various concentrations. The class selectivity of AMIPs for flavonoids was found in Acanthaceae ebracteatus. Compared with other analogs, competitive binding experiments revealed that the polymer had greater selectivity for acacetin. After AMIP solid-phase extraction (AMISPE), the linearity, LOD, LOQ, intraday and interday variabilities, recovery, and repeatability of AMIPs combined with HPLC–MS/MS were validated, confirming the method’s selectivity, precision, accuracy, and reproducibility. The contents of acacetin, apigenin, kaempferol, luteolin, quercetin, and genistein in Acanthaceae ebracteatus were determined. (Conclusions) These results indicate that AMISPE coupled with HPLC–MS/MS is a new, simple, and practical method for extracting, purifying, and enriching flavonoids from complex samples, such as those of herbs and other natural marine plants.