The quantitative analysis of nanoparticles (NPs) in the environment is significantly important for the exploration of the occurrence, fate, and toxicological behaviors of NPs and their subsequent environmental risks. Some protocols have been recommended for the separation and extraction of NPs that are potentially dispersed in complex environmental matrixes, e.g. sediments and soils, but they remain limited. However, certain factors that may significantly affect extraction efficiency have not been comprehensively explored. In this study, on the basis of the single-particle inductively coupled plasma mass spectrometry (SP-ICP-MS) technique, a simple standardized protocol for separating and analyzing metal-containing NPs in sediment samples was developed. On consideration of the extraction efficiencies of indigenous NPs (Ti- and Zn-NPs) and spiked NPs (Ag- and Au-NPs) in sediments, sedimentation with a settling time of 6 h is recommended for the separation of NPs and large particles, and the optimal sediment to water ratio, ultrasonication power, time, and temperature are 0.4 mg/mL, 285 W, 20 min, and 15-25 °C, respectively. On the basis of the optimized method, the recoveries of spiked Ag and Au-NPs were 71.4% and 81.1%, respectively. The applicability of the optimal protocols was verified, and TOC was proved to be an important factor controlling the separation and extraction of NPs in environmental samples. The separation and extraction of NPs in elevated TOC samples can be improved by increasing the ultrasonication power, time, and temperature.