A sensitive and rapid method for Bisphenol A (BPA) detection in water is always in high demand. A novel and accurate aptamer-functionalized magnetic relaxation switch (MRS) sensor was developed for the detection of BPA, which is based on the transverse relaxation time (T₂) change of water protons that originated from the dispersion/aggregation of magnetic nanoparticles (MNPs). Aptamer-functionalized MRS sensor was prepared and characterized. Based on the linear relationship between BPA concentration and the magnetic relaxation characteristic signal (including the T₂ attenuation curve, T_2W, and T₂ distribution), the mono-exponential fitting of Carr-Purcell-Meiboom-Gill (CPMG) decay (T_2W) was finally chosen as the magnetic relaxation characteristic detection signal. According to the sensing effect of the aptamer-functionalized MRS sensor for BPA, the concentration of Fe₃O₄@SiO₂ ~ Apt NPs, incubation times, and pH of the detection system were optimized to be 0.005 mg/mL, 15 min and 7, respectively. In the quantitative analysis of BPA, the detection working range was between 10 ng/mL and 100 ng/mL, and the limit of detection (LOD) was determined to be 2.9 ng/mL, which satisfied the safety limit set by China (10 ng/mL) and the European Union (0.6 mg/kg). Besides, the average recoveries of BPA in spiked water samples ranged from 92.6% to 103.1%, the intra-day and inter-day results all showed good precision (RSD values less than 15%). The results indicated that the proposed sensor could be a useful tool for sensitive and accurate analysis of BPA in water.