Nanoplastics (NPs) as emerging marine pollutants can be taken up by seafood organisms. It is crucial to quantitatively assess NP's distribution behavior in organisms to elucidate concentration dependent biological effects. Such a knowledge gap has remained due to the lack of reliable NP models and analytical methods. Herein, surface enhanced Raman scattering (SERS)-labeled NP models were developed and their bioavailability, distribution and accumulation in Ruditapes philippinarum, a typical marine bivalve, were quantitatively studied. Taking advantage of the sensitive and characteristic SERS signals of the NP models, distribution could be quickly and accurately obtained by the Raman imaging technique. Moreover, quantitative analysis of NPs could be performed by the detection of gold element contents via inductively coupled plasma mass spectroscopy (ICP-MS) detection. ICP-MS results revealed that after 3 days exposure of monodispersed NPs (100 nm, 0.2 mg L-1), the digestive gland accumulated 86.7% of whole-body NPs followed by gill (5.2%), mantle (5.1%), foot (1.3%), exhalant siphon (1.1%), and adductor (0.6%). Upon 11 days depuration, 98.7% of NPs in the digestive gland were excreted, whereas the clearance ratios in other organs were much lower. NP aggregates (around 1.5 μm) demonstrated similar distribution and clearance trends to the monodispersed ones. However, the accumulation amount in each organ was 15.2% to 77.6% lower. Surface adherence and passive ingestion routes resulted in NP accumulation, which contributed to the comparable NP abundance in these organs. Additionally, boiling treatment (mimicking a cooking process) did not decrease the NP amount in these organs. This work provided a dual-mode and quantitative analysis protocol for NPs for the first time, and suggested the risk of NP uptake by humans via bivalve seafood diets.