Samples of seven species of cephalopods and crustaceans were collected from major fish markets on the Korean coast and analyzed for mercury (Hg) using a direct Hg analyzer and for the metals cadmium (Cd), lead (Pb), chromium, silver, nickel, copper, and zinc using inductively coupled plasma mass spectrometry. The distributions of heavy metals in muscles, internal organs, and whole tissues were determined, and a risk assessment was conducted to provide information concerning consumer safety. The heavy metals accumulated to higher levels (P < 0.05) in internal organs than in muscles for all species. The mean concentrations of Cd, which had the highest concentrations of the three hazardous metals (Cd, Pb, and Hg), in all internal organs (except those of blue crab) exceeded the regulatory limits set by Korea and the European Union. The Cd concentrations in all whole tissues of squid and octopus (relatively large cephalopods), red snow crab, and snow crab exceeded the European Union limits. The estimated dietary intake of Cd, Pb, and Hg for each part of all species accounted for 1.73 to 130.57%, 0.03 to 0.39%, and 0.93 to 1.67%, respectively, of the provisional tolerable daily intake adopted by the Joint Food and Agriculture Organization and World Health Organization Expert Committee on Food Additives; the highest values were found in internal organs. The hazard index (HI) is recognized as a reasonable parameter for assessing the risk of heavy metal consumption associated with contaminated food. Because of the high HI (>1.0) of the internal organs of cephalopods and the maximum HI for whole tissue of 0.424, consumers eating internal organs or whole tissues of cephalopods could be at risk of high heavy metal exposure. Therefore, the internal organs of relatively large cephalopods and crabs (except blue crab) are unfit for consumption. However, consumption of flesh after removing internal organs is a suitable approach for decreasing exposure to harmful metals.