A modified quick, easy, cheap, effective, rugged and safe method was established for simultaneous determination of atropine, anisodamine, and scopolamine in goji berries by using ultra‐high‐performance liquid chromatography with tandem mass spectrometry. The graphene/hexagonal boron nitride hybrids were prepared and first applied as a cleanup adsorbent. Compared to classical cleanup adsorbent (C18), the graphene/hexagonal boron nitride hybrids as adsorbent had better extraction efficiency for the detection of analytes. Under the optimal conditions, the proposed analytical method achieved satisfactory linearity (R2 > 0.995), and obtained desirable recoveries ranged from 77.4 to 94.0% with the relative standard deviation of 1.2–6.1% at the concentration levels of 3.2–13.4 µg/kg. The limits of quantitation of atropine, anisodamine, and scopolamine were, respectively, 3.2, 4.6, and 4.5 µg/kg with linearity ranged from 3.2 to 25.4 µg/kg. The modified quick, easy, cheap, effective, rugged, and safe sample preparation with ultra‐high‐performance liquid chromatography and tandem mass spectrometry method was successfully applied to evaluate the safety of goji berries collected from 30 plant areas in China, suggesting its applicability and suitability for the routine analysis of three tropane alkaloids in goji berries.