Agricultural input and output status in southern Xinjiang, China is introduced, such as lack of agricultural input, low level of agricultural modernization, excessive fertilizer use, serious damage of environment, shortage of water resources, tremendous pressure on ecological balance, insignificant economic and social benefits of agricultural production in southern Xinjiang, agriculture remaining a weak industry, agricultural economy as the economic subject of southern Xinjiang, and backward economic development of southern Xinjiang. Taking the Aksu area as an example, according to the input and output data in the years 2002-2007, input-output model about regional agriculture of the southern Xinjiang is established by principal component analysis. DPS software is used in the process of solving the model. Then, Eviews software is adopted to revise and test the model in order to analyze and evaluate the economic significance of the results obtained, and to make additional explanations of the relevant model. Since the agricultural economic output is seriously restricted in southern Xinjiang at present, the following countermeasures are put forward, such as adjusting the structure of agricultural land, improving the utilization ratio of land, increasing agricultural input, realizing agricultural modernization, rationally utilizing water resources, maintaining eco-environmental balance, enhancing the awareness of agricultural insurance, minimizing the risk and loss, taking the road of industrialization of characteristic agricultural products , and realizing the transfer of surplus labor force.