Urban development always has a strong impact on the urban thermal environment, but it is unclear to what extent urbanization factors influence urban heat island intensity (UHII) in mountainous cities, and fewer studies have been conducted on the trends of long-term UHII in mountainous cities. Chongqing, as the only municipality directly under the central government in Southwest China and a typical mountainous city, is chosen as the case study. This study analyzed the interannual and seasonal variations of UHII based on the data from meteorological stations in Chongqing from 1959 to 2018 using the least-squares method and the Mann–Kendall test, and explored the relationship between urbanization factors (urban resident population, gross domestic product (GDP), fixed investments, and gross industrial output value) and UHII. The results show that the increasing rates of temperature in urban areas of Chongqing are significantly higher than those in rural areas affected by urbanization. Using the Mann–Kendall test, it is found that almost all abrupt temperature changes in Chongqing occurred after the rapid urbanization of Chongqing in the 21st century. The annual mean UHII increased from 0.1 °C to 1.5 °C during the study period, with summer making the largest contribution. It is also found that the UHII in Chongqing has increased year by year, especially after the 1980s. The increasing rates of UHII are larger at night and smaller during the day. The increasing trends of nighttime UHII are statistically significant, while those of daytime UHII are not. In addition, UHII and urbanization factors are found to be correlated using the grey relational analysis (GRA). Eventually, a comprehensive UHII index and a comprehensive urbanization index are constructed using principal component analysis (PCA). A tertiary regression model of UHII and urbanization index is established, which reflects that the UHII in Chongqing will continue to grow rapidly with the development of the city.