The village-level organization is one of the most important governing subjects in China’s rural areas. It plays an important role in the implementation of public policy and the management of regional public affairs. In order to eliminate the contradictions caused by the levy of agricultural tax, the government abolished agricultural tax in 2006, which has won praises from all circles of the society. However, it has changed the logical basis of village-level organization’s behavior, showing a phenomenon of departure from the goals of village-level organization in practice. Based on the review of relevant literature, we made a questionnaire survey on Zhejiang, Anhui, Jiangsu, Hubei, Henan, Shanxi and Chongqing provinces, combined with case studies, summarized the five forms of functional alienation of the village-level organization in the post-agricultural tax era. Village officials often left their posts and went to work or live in the city. They embezzle collective assets and win village elections by the money. Evil forces rule the village-level organization and the relationship between village officials and peasants has centrifugal tendencies. Serious consequences follow. First of all, there is a serious lack of rural public service supplied and transformed stagnation of service-oriented organization. Secondly, the role of village-level democracy has declined and the interests of the peasants maintenance mechanism have fractured. Thirdly, the foundation of the village-level organization suffers more weakness, slackness and loss of credibility. Lastly, the legitimacy of the village-level organization is in question. Based on the theory of resource dependence, the reasons for the functional alienation of village-level organization in the post-agricultural tax era are the change of external environment such as financial resources and institutional system, the internal governance resources shortage problems, the administrative assessment under the pressure system and the increasing of a utilitarian culture. According to the strategic task of the 18th National Congress of the Communist Party and the promotion to new rural construction, we give some advices to make the village-level organization return to its normal function: establishing the system of stable funds, enriching the governance resources of village-level organizations, promoting the public services, enforcing the responsibility of village officials, improving the “Sunshine Village Project”, establishing and perfecting the supervision system of village affairs, improving the structure of village-level organizations, establishing the village official exit mechanism, cultivating the rural public culture and modern civic awareness. Using questionnaire surveys and case studies, we grasp the current performance of the village-level organization, observed the functional alienation in the post-agricultural tax era, and put forward some feasible countermeasures. A limitation is that we were unable to follow different levels of economic development to classify the functional alienations of the village-organization in different areas.