With the rapid development of industrialization and urbanization, rural housing vacancy (RHV) has become an increasingly universal phenomenon in China, causing many economic and social problems. Despite many studies on RHV, relatively little attention has been paid to distinguishing the types of vacant rural houses as well as RHV in metropolitan suburbs. Drawing upon survey data from 23 sampled villages of the Nanjing metropolitan area in China, this paper differentiates RHV into permanent vacancy and temporary vacancy and analyzes the influences of location, government interventions, and the villages’ characteristics on the two types of RHV. The empirical results show that villages located in inner suburbs and with medium travel time to city centers have higher permanent RHV rates, while those located further away from city centers usually have higher temporary RHV rates. The local government’s restrictive plans and housing construction restrictions do not increase the permanent RHV rate nor temporary RHV rate, whereas supportive plans and financial investment reduce the permanent RHV rate and increase the temporary RHV rate. Permanent RHV rates are relatively lower in villages that are less reliant on agricultural development. Those villages usually have higher sublet rates of farmland, a lower proportion of agriculture laborers, and better development of manufacturing or tourism. However, temporary RHV rates do not differ significantly between agricultural villages and non-agricultural villages. The paper finds an unusual “middle bump” phenomenon of permanent RHV rate and explains it with the law of commuting circles. Some policy implications are put forward to promote the transformation and sustainable development of rural areas in China’s metropolitan suburbs.