Located in the eastern edge of the Sichuan Basin (SCB) in the southwest China, Chongqing is a mountainous region with typical complex topographic features. Using the hourly rainfall observation data of high-density 1686 meteorological stations in Chongqing during warm season from 2009 to 2016, we investigated the diurnal characteristics of precipitation affected by complex topography. The complex mountainous terrain has a significant impact on diurnal variations and distinct regional features of rainfall amount, frequency, and intensity. The stations located in the higher complex mountainous areas have greater rainfall amount, frequency, and intensity than those in the lower surrounding areas. In addition, the detailed characteristics of the rainfall amount and frequency in the four study regions further show that the rainfall amount and frequency significantly increase with the rise of elevation, especially in the area that terrain height sharply increases along the mountain extending direction. The diurnal variation of the rainfall amount is characterized by a bimodal structure with a dominant early-morning peak occurring at approximately 0700 LST (23 UTC) and a weaker secondary late-afternoon peak at approximately 1600 LST (08 UTC), while the rainfall frequency has a single early-morning peak. The terrain height has a significant impact on the proportions of the early-morning rainfall. With the elevation increasing in the four study regions, the proportions of rainfall amount (frequency) that occurs during early-morning period decrease.