Aflatoxins (AFs) have attracted increasing amounts of attention in recent years for their high toxicity. Previously, AF-polluted Chinese Patent Medicines (CPMs) were ignored, but their quality, safety, and efficacy might be influenced by the toxic compounds. The objective is to develop a simple, low-cost, and efficient method for quantitative analysis of aflatoxins B (AFB) and B₂ (AFB₂) in CPMs to ensure their safe use. A simple, modified, magnetic nanoparticle-based solid-phase extraction (SPE) combined with HPLC-fluorescence detection for the determination of trace amounts of AFB and AFB₂ was established. The main parameters affecting the efficiency of modified magnetic nanoparticle-based SPE, such as pH of sample solution, adsorbent amount, adsorption time, and desorption condition, were investigated. Under the optimum conditions, AFB and AFB₂ were linear in the ranges of 0.3-10 and 0.04-3 ng/mL with the correlation coefficient () of 0.9998 and 0.9999, respectively. Their intraday precisions were 1.16 and 2.30% and the interday precisions were 1.28 and 1.87% for AFB and AFB₂, respectively. The developed SPE was applied for AFB and AFB₂ extraction in three commercially available Fupuganmao granule samples, and the results were compared with the official immunoaffinity column chromatography method. The method provided a preferable candidate for the determination approach of AF measurement in CPMs. Amine-functionalized magnetic nanoparticles were successfully applied to SPE for adsorbing AFB and AFB₂ in CPMs for the first time.