The purpose of this study is at the following points through this integrated research (including design thinking and product architecture and organizational innovation): First, what impact will the design thinking have on the product structure and how it will be affected? Second, what impact will the design thinking bring on the organization’s innovation model and how it will affect it? Third, design thinking model of the product architecture and organizational innovation, how to create customer value and affect the business performance? This study takes quantitative research empirical analysis, and to listed in Taiwan, OTC manufacturers as the main survey respondents. The number of questionnaire was 1548 and the questionnaire recovery rate was 17.12%. This study was quantified and analyzed, and the following important findings were obtained. First, the enterprise into the design thinking will significantly affect the product architecture of the degree of standardization. Second, the introduction of enterprise design thinking will significantly affect the organizational innovation model. Third, the enterprise into the design thinking through the product architecture, and then on the organizational performance of a positive impact. Fourth, the enterprise into the design thinking through organizational innovation model, and then on the organizational performance of a positive impact. Finally, the construction is suitable for Taiwan enterprises leading product architecture and create organizational design ideas.