Abstract: Agriculture is the foundation of the national economy. The scientific and technological innovation of agriculturerelated enterprise in Qingliu, an agricultural County in mountainous area of northwest Fujian, is important for the economic development there. In this paper, the development situations of agricultural enterprises in Qingliu were analyzed, and the existing problems in process of innovation were summarized, which included weak consciousness, low innovation ability, insufficient research and development investment, shortage of technical talents, and so on. Then the corresponding countermeasures were put forward, such as increasing research investment, strengthening the cultivation of talents, enhancing the intellectual property protection, improving informatization level of agricultural enterprises, etc.