The Trans-Pacific Partnership Agreement (TPP) is a regional free trade agreement of broad scope and comprehensive coverage with high-standard disciplines. Under the current TPP agreement, tariffs on fish and fishery products will ultimately be fully eliminated. To support the liberalization effort, this study utilizes a price-endogenous mathematical-programming-based Taiwan fishery sector model (TFSM) to evaluate the potential impact of eliminating tariffs on fishery production and consumption in Taiwan. This qualified support for liberalization stems from production systems for fish being highly heterogeneous and subject to extensive levels of management and border protection. The average nominal tariff rate is 19.85% for Taiwan’s fishery products (HS 03), which is much higher than the average tariff of TPP members’ fishery products, 3.62%. Thus, the tariff elimination is expected to enlarge the fishery import significantly. Thus, the removal of low tariff barriers cannot stimulate more export for Taiwan’s fishery products. We use the UN FAO database and Taiwan’s official data to compare the highest import price and lowest export price of all fishery products between TPP members and Taiwan. The result shows that the total production value of fishery sector will be reduced by 3.90%, in which the potential import products increased by 104.52% and the potential export reduced products by 5.77%. The tariff elimination would also reduce the domestic price of fishery products. For example, the production of saury, mackerel, clams and other offshore and coastal fish reduced more than 10.23%, while the import of these product increased 10~15%. Thus, the government has to negotiate a reasonable transitional period for implementing structural reforms in response. Meanwhile the fishery industry has to enhance their operational efficiency to meet the challenges of globalization and high-standard free trade agreement.