The advantageous natural environment and climate plus long term policy supported by the government has bred prosperity of agricultural industry in Taiwan. However, failing to acknowledge the importance of agricultural intellectual property timely has put such prosperity in a down slope. For example, the frequent agricultural exchange and cooperation between the two sides of the Taiwan Strait in recent years, has led to considerable increase of agricultural investment shifting from Taiwan to Mainland China. Such outflow of agricultural intellectual property is apparently causing negative impacts on the continual development of agriculture in Taiwan. It is therefore, necessary to raise concerns and figure out strategy for the protection and management of agricultural intellectual property from within the island. First of all, this study would brief the history of cross-strait agricultural exchange and some theories of the management of agricultural intellectual property in the past. Followed by that would be the discussion of current regulations in relation to the protection of agricultural intellectual property right. Then this study would introduce two cases of the management of agricultural intellectual property of two foreign companies for practical reference. Furthermore, this study would present two cases of interview conducted in two different Taiwanese agricultural firms as a methodological approach to unwind the problems and difficulties in practical business investment. Analysis on current strategic management of agricultural intellectual property either in Taiwan or abroad would be addressed. Finally, by focusing on the two facets (a) the solution of agricultural exchange policy and (b) entrepreneurial management, we propose a better mechanism of protecting and managing agricultural intellectual property for future reference when Taiwan intends to increase agricultural investment in Mainland China.