Although there has been a rapid urbanization in China since the 1980s, the simultaneous urban shrinkage phenomenon has existed for a long time. The study of shrinking cities is particularly important for China as the current urban development has changed from physical expansion to built-up area improvement. After redefining what constitutes a city (what we term a natural city), we compared the adjusted nightlight intensity of National Polar-orbiting Partnership Visible Infrared Imaging Radiometer Suite (NPP-VIIRS) data between 2013 and 2016 to accurately identify shrinking cities throughout China. The results indicate that there are 2,862 redefined natural cities in China and that the total area reaches 53,275 km², about 0.5% of the national territory. Based on this, we identified 798 shrinking cities with a total area of 13,839 km². After analyzing the relative position of shrinking cities and internal shrinking pixels in the geometric space, the morphological characteristics of shrinking cities were systematically classified into six patterns. The majority of shrinking cities belong to scatter shrinkage, central shrinkage, and local shrinkage; only 5% are complete shrinkage; the rest are unilateral shrinkage and peripheral shrinkage. In addition, six shrinkage causes were quantitatively classified and summarized by referring to multiple-source urban data and municipal yearbooks. To enrich the methodological system for urban shrinkage, the research provides a reminder of the need to consider the other side of urbanization (i.e., dissolution of social networks) and proposes appropriate strategies and policies to address shrinkage issues.