The study uses the fuzzy Delphi and FANP (fuzzy analysis network process) methods to integrate the views of experts from enterprises and academia regarding the future direction of the agricultural biotechnology industry in Taiwan, in order to extract the critical success factors influencing its transformation. This study compares the differences in the “cross-domain” and “non-cross-domain” critical success factors, and expects that the research results could be a decision-making reference for both the industry and the government. The research results show that the cross-domain critical factor that influence the transformation of the agricultural biotechnology industry in Taiwan are sequentially: a stable source of raw materials, control of the trend of market demand, a new production equipment, the capability in supporting upstream and downstream industries, the integration of the human resources of the upstream, midstream, and downstream industries, and the capability in marketing and promotion. The non-cross-domain critical factors are sequentially: the capacity to establish the system of product technology, the capacity to control intellectual property rights, a perfect educational system, the capacity to carry out risk management of the new product development, the competence in cultivating the capacity of technical and R&D personnel, and laws and regulations.