Micro- and nanoplastics unavoidably enter into organisms and humans as a result of widespread exposures through drinking waters, foods, and even inhalation. However, owing to the limited availability of quantitative analytical methods, the effect of nanoplastics inside animal bodies is poorly understood. Herein, we report a sensitive and robust method to determine the chemical composition, mass concentration, and size distribution of nanoplastics in biological matrices. This breakthrough is based on a novel procedure including alkaline digestion and protein precipitation to extract nanoplastics from tissues of aquatic animals, followed by quantitative analysis with pyrolysis gas chromatography-mass spectrometry. The optimized procedure exhibited good reproducibility and high sensitivity with the respective detection limits of 0.03 μg/g for polystyrene (PS) nanoplastics and 0.09 μg/g poly(methyl methacrylate) (PMMA) nanoplastics. This method also preserved the original morphology and size of nanoplastics. Furthermore, to demonstrate the feasibility of the proposed method, 14 species of aquatic animals were collected, and PS nanoplastics in a concentration range of 0.093-0.785 μg/g were detected in three of these animals. Recovery rates of 73.0-89.1% were further obtained for PS and PMMA nanospheres when they were spiked into the tissues of Zebra snail and Corbicula fluminea at levels of 1.84-2.12 μg/g. Consequently, this method provides a powerful tool for tracking nanoplastics in animals.