台灣得天獨厚的地理環境及氣候，及長久以來政府對農業的輔導與支持，造就了發達的農業產業。然而以往對於農業智慧財產權重要性的忽視，也使得台灣農業優勢逐漸喪失。近年來隨著兩岸農業交流互動頻繁，台商前往大陸進行農業投資日多，農業智慧財產亦隨之外流，反向衝擊台灣農業發展，值此之際，確有重新審視兩岸農業智慧財產保護與經營的必要性。本文將首先從兩岸農業交流之歷史沿革及現有之農業智慧財產經營概念作一背景介紹，繼而探討農業智慧財產保護之特點與現行兩岸農業智慧財產相關法規之異同，並提出兩家國外企業經營農業智慧財產之模式以了解實務上經營農業智財之差異；其次將透過實際訪談兩家皆在台灣與大陸投資之農企業，瞭解實務上在台灣與大陸經營農業智慧財產時所面臨的問題與困境，並以之與國外企業經營之法比較，探討農企業在台灣或大陸經營農業智慧財產之對策；最後總結上述實務與理論之意見，從現有兩岸農業交流政策之因應及企業經營面向兩方面加以探討，提出農企業在台灣與大陸進行農業投資時在農業智慧財產保護與經營方面之建議。 The advantageous natural environment and climate plus long term policy support 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.