In cases of low concentration paraquat (PQ) poisoning, as the disease progresses over a long period of time, the prototype PQ may not be detected in the urine, which has a significant negative impact on the precise treatment of the poisoning. But PQ poisoning can also be confirmed by the detection of specific metabolites of PQ in the urine samples. In the present study, core-shell amphiphilic carboxyl-functionalized magnetic polymer microsphere (Amphiphilic-MPs-COOH) was prepared, and the as-prepared Amphiphilic-MPs-COOH was characterized by transmission electron microscope (TEM), scanning electron microscope (SEM), Fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and thermogravimetry and differential thermogravimetry analyses (TG-DTG). Then, the Amphiphilic-MPs-COOH was employed as a magnetic solid-phase extraction (MSPE) adsorbent for pretreatment and rapid determination of PQ and its four metabolites from urine samples prior to ultra-high performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS). The extraction-elution conditions of Amphiphilic-MPs-COOH towards PQ and its metabolites were optimized in spiking urine samples to obtain the best MSPE efficiency. The adsorption mechanism of PQ and its metabolites by Amphiphilic-MPs-COOH involves electrostatic attraction and π-π stacking interactions. Moreover, the effect of different ratios of hydrophilic monomer NVP and functional monomer 4-VBA on the extraction and purification performance of PQ and its metabolites in urine samples. And the results revealed that both hydrophilic monomer and functional monomer were important for the adsorption of PQ and its metabolites, and the addition of the appropriate amount of the hydrophilic monomer NVP can improve the compatibility of the adsorbent with the urine substrate. In addition, this study compared the matrix effect of the Amphiphilic-MPs-COOH based MSPE method and the commercial Waters Oasis WCX SPE method. The results showed that the Amphiphilic-MPs-COOH based MSPE method developed in this paper had better resistance to matrix interference. Under optimal conditions, the recoveries of PQ and its metabolites were ranging from 84.5 to 103%, with relative standard deviations (RSDs) of 1.1–6.3%. While the limits of detection (LODs, S/N ≥ 3) and limits of quantification (LOQs, S/N ≥ 9) of the method were in range of 0.1–1.6 μg/L and 0.3–4.8 μg/L, respectively. Finally, the established MSPE-UPLC-HRMS method in this study was used to confirm PQ poisoning not only based on detecting PQ prototype, but also on its four metabolites, providing strong technical support for clinical precision treatment.