A system is disclosed for monitoring payload at a worksite having multiple machines. The system may have a first sensor located onboard a haul machine and configured to generate a first signal indicative of a total amount of material in the haul machine, and a second sensor located onboard a load machine and configured to generate a second signal indicative of an amount of material being dumped into the haul machine by the load machine. The system may also have at least one controller in communication with the first and second sensors. The at least one controller may be configured to selectively perform a sensor calibration process based on a comparison of the first and second signals.