A method is disclosed for calibrating a vehicle model used to autonomously control a machine on a worksite. The method may include measuring a first value indicative of an operating condition of the machine, predicting a second value, using the vehicle model, corresponding to the first value and indicative of the operating condition, and determining a difference between the first value and the second value. The method may also include autonomously directing the machine to a calibration site of the worksite in response to determining that the difference between the first value and the second value is greater than a predetermined threshold, wherein the calibration site is automatically selected from a plurality of locations at the worksite based on a suitability index of the calibration site.