Based on the results of existing research, typical urban problems can be divided into three categories—traffic congestion, resources shortage, and environmental pollution. This study used cross-section data of 204 Chinese prefecture-level cities in 2013 to build a population spatial distribution index on the basis of nighttime light data for an empirical study. First, ordinary least squares (OLS) regression was applied to examine the impacts of city size, spatial imbalance, lagged infrastructure construction, industrial transformation, and institutional obstacles on urban problems. Second, a threshold effect model was constructed to further investigate possible nonlinear relationships between the influencing factors and urban problems. The empirical results prove that the various aspects of urban problems should be attributed to different influencing factors since these problems are complex. The main reasons leading to traffic congestion are big city size and centralized distribution of urban population, as well as the lack of transportation infrastructure. While resources shortage is not a universal problem in most big cities, in contrast, the improvement of industrial structure, increasing supply of public services, and concentration of administrative power are helpful for big cities to attract and bring in resources. The expansion of urban population and the agglomerated structure of population distribution both hinder environmental pollution control. Besides, the growth in the proportion of non-agricultural industries and expansion of urban road area both can damage urban ecosystems.