The double-level rural business system, “the combination of unified and separated business system”, built based on contracted land system of a family at the initial period of reform and opening-up of China makes the traditional agriculture production methods of “small production” continue after the “separation”, but rural property ownership does not make basic change, which leads to the difficulty in the introduction of modern agricultural production factors. Thus, the modernized reconstruction of the traditional agriculture can not be smoothly implemented. The practice in rural business system innovation of Sichuan Province shows that currently, the main body of China’s agriculture production and business becomes more and more diversified, that both agricultural specification and diversification exist in the production and business of the households, and that rural property right system is still the main barrier of the institutional innovation though the institutional evolution method from bottom-up makes rural business system innovation diversified. As a result, China’s rural business system innovation should stick to “the separation” and innovate “the unification”, the core issue of the reform lies in the level of “the unification”, and the key to the problem is to overall boost rural property right system reform.