It is argued that the reason for poor performance of research in various domains of social science in Taiwan is caused by the fact most that researchers understand neither the progress and development of major academic paradigms in contemporary Western civilization, nor their own cultural tradition. They imported popular research methods from the West and followed the approaches in such a similar way that they lost their own academic identities eventually. The article reviewed my previous works of research in the passed two decades, advocated that it is necessary to integrate two types of study for the development of social science in Confucian society: First, to comprehend the major academic paradigms developed in Western civilization; Second, to study the manifestations of Confucian cultural traditions in the contemporary societies by academic paradigms from the West. In order to achieve this goal, it is recommended that the philosophy of science and the progress of major academic paradigms should be included in the training program for graduate students, so that they are able to use it as horizon for conducting innovative research works and developing their academic careers.