Solid phase extraction has been increasingly applied for the detection of organic micropollutants (OMPs). However, time-consuming and high-cost disadvantages also limit the widespread use of this method, especially for the extraction of large-volume field water samples. In this study, a gas chromatography-mass spectrometry (GC-MS) method based on the magnetic microsphere (M150) solid-phase-extraction (MSPE) was established to investigate the OMPs in source water throughout the whole Huai River. In brief, the results demonstrated that the extraction efficiency of the M150 was superior to that of C18 and HLB for the selected OMPs, including species of polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs), phthalate esters (PAEs) and nitrobenzenes (NBs), and the method detection limits of M150 for these OMPs were comparable to those of C18 and HLB. The optimized conditions of extraction and elution were the 100 mg/L dosages of microspheres, extraction time of 60 min and pH of 2, and the eluent with a similar polarity, hydrophobicity and molecular structure to the OMPs rendered higher elution efficiencies. A total of 21 types of OMPs affiliating to PAHs, OCPs, PAEs and NBs were detected by the established method, with the total concentrations of 505-2310 ng/L in source water of the Huai River. Spatial differences of the OMPs were also observed, demonstrating the link between pollutant profiles and geographical locations. This study provides an alternative to enrich OMPs in filed water samples, and it reveals pollutant profiles of source water throughout the whole Huai River.