A worksite management system for use with a mobile machine is disclosed. The worksite management system may have a control module located onboard the mobile machine and configured to store a least one operational relationship, and an offboard controller located at a worksite of the mobile machine in communication with the control module. The offboard controller may be configured to generate an analysis of machine performance at the worksite. The offboard controller may be further configured to cause remote reconfiguration of the at least one operational relationship based on the analysis to positively affect performance of the mobile machine.