As a sustainable substitute for non-renewable mineral resources and solid waste landfilling, municipal solid waste incineration residues (MSWIRs) are useful in road pavements. This study investigates the thermal characteristics and temperature distribution of flexible pavements containing MSWIRs with hollow microsphere structures. First, the volumetric properties of asphalt mixtures containing MSWIR fillers were measured. The effects of MSWIRs on the mixture’s physical characteristics were investigated in terms of thermal conductivity, specific heat capacity, and thermal diffusivity. A three-dimensional finite element model incorporating surface thermal conditions was established and validated to analyze the internal temperature distribution and heat transfer behavior within the asphalt. Finally, the high-temperature conditions of summer were simulated in an indoor irradiation test to evaluate the risk of heat islands in urban areas. The results showed that the mixture containing MSWIRs exhibited a higher specific heat capacity (from 0.8385 to 0.9554 J/(kg·K)) and lower thermal conductivity (from 1.4356 to 1.1362 W/(m·K)) than the reference mixture with limestone filler. Therefore, it contributed to a lower heat flux distribution within the pavement. However, the increase in asphalt surface temperature caused by MSWIRs may exacerbate the urban heat island effect in the summer, which should be considered before using road materials containing MSWIRs.