There is a growing concern about the effects of nanoplastics on biological safety and human health because of their global ubiquity in the environment. Methodologies for quantitative analysis of nanoplastics are important for the critical evaluation of their possible risks. Herein, a sensitive yet simple and environmentally friendly extraction approach mediated by protein corona is developed and coupled to pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) for nanoplastic determination in environmental waters. The developed methodology involved the formation of protein corona by addition of bovine serum albumin (BSA) to samples and protein precipitation via salting out. Then, the resulting extract was directly introduced to Py-GC/MS for nanoplastic mass quantification. Taking 50 nm polystyrene (PS) particles as a model, the highest extraction efficiency for nanoplastics was achieved under the extraction conditions of BSA concentration of 20 mg/L, equilibration time of 5 min, pH 3.0, 10% (w/v) NaCl, incubation temperature of 80 °C, and incubation period of 15 min. The extraction was confirmed to be mediated by the protein corona by transmission electron microscopy (TEM) analysis of the extracted nanoplastics. In total, 1.92 and 2.82 μg/L PS nanoplastics were detected in river water and the influent of wastewater treatment plant (WWTP), respectively. Furthermore, the feasibility of the present methodology was demonstrated by applying to extract PS and poly(methyl methacrylate) (PMMA) nanoplastics from real waters with recoveries of 72.1-98.9% at 14.2-50.4 μg/L spiked levels. Consequently, our method has provided new insights and possibilities for the investigation of nanoplastic pollution and its risk assessment in the environment.