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Building performance simulation can be used for retrofit analysis. However, it is time-consuming to create building energy models for existing buildings. This paper presented and implemented a rapid building energy modeling method for existing buildings by using prototype models and automatic model calibration for retrofit analysis with uncertainty. A shopping mall building located in Changsha, China, was selected as a case study to demonstrate the rapid modeling method. First, a toolkit named AutoBPS-Param was developed to generate building energy models with parameterized geometry data. A baseline EnergyPlus model was generated based on the building’s basic information, including vintage, climate zone, total floor area, and percentage of each function type. Next, Monte Carlo sampling was applied to generate 1000 combinations for fourteen parameters. One thousand EnergyPlus models were created by modifying the baseline model with each parameter combination. Moreover, the 1000 simulation results were compared with the measured monthly electricity and natural gas usage data to find 29 calibrated solutions. Finally, the 29 calibrated energy models were used to evaluate the energy-saving potential of three energy conservation measures with uncertainty. The retrofit analysis results indicated that the electrical energy saving percentage of chiller replacement ranged from 1.57% to 13.51%, with an average of 8.27%. The energy-saving rate of lighting system replacement ranged from 1.92% to 11.66%, with an average of 6.43%. The energy-saving rate of window replacement ranges from 0.31% to 1.81%, with an average of 0.55%. The results showed that AutoBPS-Param could rapidly create building energy models for existing buildings and can be used for retrofit analysis after model calibration.