This application discloses a communication method, an optical line terminal, and an optical network unit in a passive optical network system. The PON system includes an OLT and at least one ONU, and the method includes: receiving, by the OLT, a first message that is sent by a first ONU in the at least one ONU through a first upstream channel; determining a first round trip time (RTT) of the first ONU based on a receiving moment of the first message; determining a time window based on the first RTT; sending first indication information to the first ONU through a downstream channel, where the first indication information includes the time window; receiving a second message that is sent by the first ONU through a second upstream channel within the time window; and determining a second RTT of the first ONU based on a receiving moment of the second message.