There are various explanations for the centralization of planning approval authority, but few studies focus on the explanation of selective centralization from a national governance perspective. To address this gap, this paper uses the concept of land risk to identify the reason why central government centralizes the planning approval authority of a prefectural-city in China. An econometric quantitative approach is adopted. The findings suggest that land risk from farmland protection is an important factor affecting centralization. Specifically, the probability of centralization increases by approximately 2% for each unit reduction in per capita farmland area, by 1.6% for every 1% increase in land transfer area and by 1% for each level increase in illegal land use. Furthermore, the cities with high land risk are mainly concentrated in four provinces along eastern coastal China. Additionally, the result is predicted with an overall accuracy of 93%, which proves the validity of the model.