This dissertation provides a thorough analysis of the impact of international trade policy on agricultural input markets. International agricultural trade are often affected by policies in importing and exporting countries. These policies can be directly or indirectly imposed on the production inputs. It is important to understand the markets’ responses in both importing and exporting countries to the policies changes through vertical linkages between the input and output markets. This dissertation provides three essays to study this topic from the prospective of importer, exporter, input market, output market, and trade negotiation mechanism. Essay 1 studies a European Union trade policy induced technological innovation, specifically on its impact on the U.S. apple markets. I adopt the Ex Ante approach to simulate the market reaction to both the European Union policy change and the technological innovation. The research finds that the policy induced technological innovation benefits the outputs that are intensive in the policy affected input. The methodology and conclusion contribute to research on markets with highly differentiated products. Essay 2 is motivated by the decade-long cotton dispute between Brazil and the United States. The dispute was arbitrated based on several domestic policies of the United States. This chapter analyzes the impact of a U.S. domestic policy on 1) land re-allocation with a difference-in difference model; 2) international cotton trade between the United States and the rest of world including Brazil with a partial equilibrium simulation model. Based on the analysis, I find limited policy impact of removing this particularly U.S. domestic policy on international cotton trade. The result is consistent to the World Trade Organization arbitration of the dispute. Essay 3 summarizes three most common methods of quantifying the trade impact of non-tariff trade measures in the literature. I carefully compare the advantages and disadvantages between each method. A guidance of how to choose an appropriate method based on the characteristic of a non-tariff trade measure is summarized. To illustrate the guidance, I show a real example of apple trade with non-tariff trade measure imposed by the European Union.