Metal nanoparticles (NPs) determination has recently attracted considerable attention because of the continuing boom of nanotechnology. In this study, a novel method for separation and quantitative characterization of NPs in aqueous suspension was established by coupling thin layer chromatography (TLC) with laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Gold nanoparticles (AuNPs) of various sizes were used as the model system. It was demonstrated that TLC not only allowed separation of gold nanoparticles from ionic gold species by using acetyl acetone/butyl alcohol/triethylamine (6:3:1, v/v) as the mobile phase, but it also achieved the separation of differently sized gold nanoparticles (13, 34, and 47 nm) by using phosphate buffer (0.2 M, pH = 6.8), Triton X-114 (0.4%, w/v), and EDTA (10 mM) as the mobile phase. Various experimental parameters that affecting TLC separation of AuNPs, such as the pH of the phosphate buffer, the coating of AuNPs, the concentrations of EDTA and Triton X-114, were investigated and optimized. It was found that separations of AuNPs by TLC displayed size dependent retention behavior with good reproducibility, and the retardation factors (R(f) value) increased linearly with decreasing nanoparticle size. The analytical performance of the present method was evaluated under optimized conditions. The limits of detection were in the tens of pg range, and repeatability (RSD, n = 7) was 6.3%, 5.9%, and 8.3% for 30 ng of 13 nm AuNPs, 34 nm AuNPs, and 47 nm AuNPs, respectively. The developed TLC-LA-ICP-MS method has also been applied to the analysis of spiked AuNPs in lake water, river water, and tap water samples.