In this paper, Cu2+ functionalized Fe3O4@polydopamine core-shell (Fe3O4@PDA@Cu2+) magnetic microspheres were prepared by the chelation between Cu2+ and catechol of polydopamine surface. The synthetic magnetic adsorbent was characterized by Fourier transform infrared spectroscopy, energy dispersive X-ray spectroscopy, vibrating sample magnetometry, thermogravimetric analysis, scanning electron microscope and transmission electron microscopy. Four purines include guanine, adenine, hypoxanthine and xanthine were selected as model compounds to evaluate the applicability of this adsorbent. Several parameters that effected the extraction efficiency, such as extraction time, adsorbent amount, solution pH, ionic strength, eluent type, concentration of eluent and eluent time, were investigated. Under the optimized conditions, good linearity was obtained with correlation coefficients between 0.9983 and 0.9999 for the four analytes, and their LOD and LOQ were 0.42–2.15 ng/mL and 1.41–6.50 ng/mL, respectively. Meanwhile, the RSDs of intra-day and inter-day precision were in the range of 1.43%–5.55% and 4.56%–7.01%, respectively. The spiked recoveries of four purines in real sample were 70.01%–102.42%, indicating this proposed method might have potential applications for the analysis of purines in real samples. In addition, the developed method was used to monitor the concentrations of adenine in rat plasma at different time points after intragastric administration.