Abstract: By taking the papers, S&T awards, patents, and extra-earnings as the indicators of output performance for an agricultural research institution, the distribution characters of them is found. Then the influence factors on the output performance for an agricultural research institution are also analyzed using a multiple regression analysis model. The conclusions on the empirical analysis are as follows: (1) Output performance of agricultural research institution shows the significant accumulation effect; (2) Output performance of agricultural research institution is effected by the scale and structure of S&T input, and technical personnel are the most important S&T resource; (3) Output performance has a close relation with the economic development factors and agricultural resource condition, and the further apart a scientific output indicator is from the agricultural production, the less it is affected by the regional economic environment; (4) Output performance is disconnected from the agriculture production. Finally, some measures and suggestions are also put forward.