Many developed countries need to plan urban policies based on multidimensional factors related to population change. However, empirical research has been inconsistent with respect to identifying these factors, including economic-, social-, and urban-planning-related factors. The purpose of this study is to clarify the nonlinear multidimensional factors that are correlated with population changes according to the city size. In the analysis, the population change rate was defined as the outcome variable, and 269 economic, social, and educational index (ESE index) were used as predictor variables. Data were stratified according to three city sizes. Using the ESE index, the XGBoost algorithm was used to analyze the nonlinear relationship between the population change rate and multidimensional data. As a key result, population changes were strongly correlated with social-related indicators, such as the population change rate among persons ages 0–14 years in small-sized cities, the natural population change rate in medium-sized cities, and the migration change rate in large-sized cities. Regarding the population decline, Japan has 1304 shrinking cities, which are primarily comprised of medium-sized and small-sized cities. In such cities, other than social-related factors, population changes correlated with the financial strength index as an economic-related factor in medium-sized cities and the designation of underpopulated areas as an urban-planning-related factor in small-sized cities. Among the multidimensional factors, cities of different sizes were characterized by factors other than social-related indicators. These multifaceted factors could provide preliminary insights for urban policymakers to explore various policy measures on which they need to focus, depending on the city’s size.