To solve the problem that the channel conditions in asymmetric cooperative FSO communication systems are not fully utilized, and the data reliability deteriorates due to high-order modulation, we proposed a layered modulation, joint physical-layer network coding scheme. In this scheme, we first designate the data priority of the information to be transmitted at the source node. Then, the transmission power of different proportions is allocated to the data based on its priority. Then, the modulated data is sent to each node, and physical-layer network coding is performed on the received data at the relay node. Finally, the relay node sends the encoded information to the destination node, and the destination node recovers the original information using the physical-layer network coding scheme. The simulation results showed that when the average signal-to-noise ratio of the channel was 15 dB, the BER of the cooperative FSO communication system could be reduced to below 10−8. In the strong atmospheric turbulence channel, the cooperative FSO communication system can obtain a signal-to-noise ratio gain of about 1.5 dB. Under strong atmospheric turbulence, this scheme could also improve the average channel capacity performance of a cooperative FSO communication system.