The leachate collection system (LCS) is an important component of barrier systems in municipal solid waste (MSW) landfills. LCS Failure due to clogging could lead to leachate accumulation, potential soil and groundwater pollution and slope failure. LCS clogging is generally ascribed to particle deposition, biofilm growth, and calcium carbonate precipitation, while temperature strongly influences microbial activity and thus inevitably affects the clogging process of LCSs. However, the role of temperature in the process of clogging and leachate accumulation in LCSs remains unclear. The main objective of this study was to bridge this research gap by developing reasonable mathematical models and comprehensively analyzing this issue. The mathematical model involved leachate flow, solute migration, physical–chemical-biological clogging, and heat transfer processes. By conducting a series of numerical simulations, the temperature variation, clogging development, and corresponding leachate accumulation inside the system during long-term operation in both the geotextile and gravel layers were numerically analyzed and predicted. The results demonstrated that, in the gravel layer, due to the higher temperature, more thorough microbial substrate consumption led to higher production of carbonate ions and hence faster and more notable calcium carbonate precipitation. Overall, the bioactivity changes due to high temperatures could considerably accelerate the failure of LCS.