The invention belongs to the field of BeiDou satellite navigation and communication technology, and particularly relates to an IAP technology-based remote upgrading system of a Beidou user machine and an upgrading method thereof. The remote upgrading system comprises a system upgrading platform, the to-be-upgraded Beidou user machine and a Beidou satellite system. A Beidou communication application message used for upgrading is output from an output end of the system upgrading platform, and is transmitted to an input end of the to-be-upgraded Beidou user machine through the Beidou satellite system. On the basis of the remote upgrading system, IAP technology is utilized to realize that when functions of the Beidou user machine are expanded, software upgrading thereof does not need to carry out power-off and dismantlement on the user machine, functional software updating of the Beidou user machine can be directly realized through the upgrading method, and the problem that remote software upgrading of the Beidou user machine is difficult is effectively solved.