Bioaccessibility of short chain chlorinated paraffins (SCCPs), which is important for estimation of dietary exposure, has not been evaluated in previous studies. In the present study, we determined the bioaccessibility of SCCPs in meat (pork, beef and chicken) and seafood (fish, clams, and prawns) using the colon-extended physiologically based extraction test as an in vitro model. The bioaccessibility percentages (BAs) ranged from 33% to 84% in the fed state and from 41% to 63% in the unfed state. The BAs observed in the fed state were lower than in the unfed state in most samples, except for pork sample, which had the highest lipid content. This could be attributed to the effects caused by dietary components added in the fed state. The effects of lipid and protein in samples on bioaccessibility were investigated. In food with a high lipid content, like pork in this study, lipid was the main factor controlling SCCP bioaccessibility. In the other five foods, which had low-medium lipid contents, BA in the unfed state was positively correlated with lipid content (p < 0.05) and negatively correlated with the protein-to-lipid content ratio (p < 0.05). No significant relationships between lipid and protein content and BA were found in the fed state. As to SCCP congener groups, a positive relationship between the BAs of SCCP congener groups and their octanol-water partition coefficients (log Kow) was found in pork sample in the fed state (p < 0.05). The BAs obtained in samples from fish, prawn, clam, and pork in the unfed state and that obtained in clam sample in the fed state were negatively correlated with log Kow (p < 0.05). We calculated more accurate estimated dietary intakes of SCCPs using our SCCP bioaccessibility data. These results will contribute to more reliable dietary risk assessments of SCCPs.