Counties are the oldest and most stable level in China's administrative regionalization system. However, in the process of China's rapid transformation from traditional society to modern society, the number of counties is shrinking on a large scale. It is of great significance to study the shrinkage of county organization system for exploring the way out of counties in the process of urbanization. In this study, nearest neighbor index and shrinkage coefficient were used to study the shrinkage of county organization system in China since the reform and opening up. The research shows that the shrinkage of counties in China is closely related to the historical process of reform and opening up, and has obvious stage characteristics. In terms of the contraction characteristics, the contraction of counties is significantly concentrated in coastal areas along the Yangtze River and cities above the sub-provincial level. Compared with the eastern region and cities above the sub-provincial level, the contraction of prefecture-level cities and counties in the central and western regions is obviously more difficult, and there are a large number of concentrated distribution of counties in some regions; On the shrinking path, the county shrinking experienced three waves of withdrawing county and setting up prefecture-level city, changing county to county-level city and changing county to municipal district, gradually advancing from coastal to inland. Due to the difference of development stage in each region, there appeared a complex situation of different shrinking types coexisting; In terms of contraction effect, county contraction has a significant positive effect on economic and social development. In terms of influencing factors, the cancellation of a county is greatly affected by the policy factors, including the change of regional development strategy, the implementation of the municipal county management system, the suspension of county to city approval, and the change of urban development policies. In addition to policy factors, the cancellation of a county is also significantly affected by its own factors, including high-level organizational structure, level of economic development, strengthening border governance, spatial location, unreasonable adjustment and callback, etc. The contraction of county organizational structure is the result of the combined action of policy factors and its own factors.