The invention provides a method and a system for determining an end time of uplink back propagation in a mobile communication system to solve a problem of accurately judging the end time of uplink back propagation, wherein the method includes the following steps: sending data with consecutive sequence numbers in a buffer of a packet data convergence protocol (PDCP) module to a serving gateway (S-GW) via an S1 tunnel; sending data with inconsecutive sequence numbers, which is from data with a first inconsecutive sequence number to last data in the buffer of the PDCP module, to a target base station via an uplink back propagation tunnel; generating an end marker datagram; sending the end marker datagram to the target base station via the uplink back propagation tunnel; and receiving, by the target base station, the end marker datagram and determining that the uplink back propagation has ended.