This paper examines the health risks of exposure to methylmercury (MeHg) through the consumption of mercury-contaminated seafood in Taiwan, based on the total diet study (TDS) method. Samples of seafood (n = 140) were purchased at fishing harbors or supermarkets and classified into seven categories (pelagic fish, inshore fish, farmed fish, shellfish, cephalopods, crustaceans, and algae). For each sample, we analyzed raw and cooked versions and compared the concentration difference. Total mercury (THg) was detected at the highest rate and in the highest concentrations in pelagic fish, followed by inshore fish and other farmed fish. The average concentration of THg was higher after cooking. In a 75th percentile scenario, the hazard indices for children aged 1 to 3 years and children aged 4 to 6 years were higher than 100% of the provisional tolerable weekly intake. Taking into consideration the risk assessment results, MeHg concentrations, and the nutritional composition of fish, we have provided weekly consumption advisories for children aged 1 to 3 years, children aged 4 to 6 years, and childbearing women aged 19 to 49 years. The weekly consumption advisories for childbearing women are 35 g/week of pelagic fish and 245 g/week of inshore fish based on the risk results from MeHg and the potential benefits from eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) intake.