The paper analyzes the basic situation for the formation of innovative rural organizations with the form of self-organization; revels the features of self-organization, including the four aspects of openness of rural organization, innovation of rural organization is far away from equilibrium, the non-linear response mechanism of rural organization innovation and the random rise and fall of rural organization innovation. The evolution mechanism of rural organization innovation is reveled according to the growth stage, the ideal stage, the decline and the fall stage. The paper probes into the basic restriction mechanism of the self-organization evaluation of rural organization from three aspects, including target recognition, path dependence and knowledge sharing. The basic measures on cultivating the innovative mechanism of rural organization are put forward. Firstly, constructing the dissipative structure of rural organization innovation; secondly, cultivating the dynamic study capability of rural organization innovation system; thirdly, selecting the step-by-step evolution strategy of rural organization innovation system.