Taking agricultural organization in China's southwestern mountainous regions as research object, on the basis of analysis of the status quo of agricultural organization development in China's southwestern mountainous regions, we use related theoretical knowledge on economics and organization science, we probe into the process of innovation and mechanism of action concerning the structure of agricultural organization in China's southwestern mountainous regions over the past 30 years. Finally we draw several general conclusions regarding structure innovation of agricultural organization in China's southwestern mountainous regions as follows: first, the structure innovation of agricultural organization, a gradual process, proceeds ceaselessly along with ongoing progress and development of agriculture, and in this process, farmers always play a fundamental role; second, the structure innovation of agricultural organization is affected by many factors, and government institutional arrangement and change in market conditions is undoubtedly the most critical factor; third, the probable evolving direction of structure innovation of agricultural organization includes internal differentiation of the same form of agricultural organization, association of different forms of agricultural organization, and emergence of other forms of agricultural organization.