Construction of a relative geologic time (RGT) volume is vital to seismic geomorphological and sedimentological interpretation. Seismic instantaneous phase unwrapping provides an excellent approach for generating an RGT volume. Although several 2D or 3D seismic phase unwrapping results have been published, there is a clear need for discussions on concrete methods for seismic phase unwrapping. We have developed the graph-cut phase unwrapping method, which performs well in the interferometric synthetic aperture radar image processing. It has advantages of strong discontinuity-preserving ability and high computing efficiency. To make it suitable for 3D seismic phase unwrapping, the method is improved by extending it from 2D to 3D, and by introducing the seismic horizon and unconformity constraints. The strong and continuous conformable seismic events, which can be easily tracked by certain autopicking methods, are introduced as horizon constraints for guiding the phase unwrapping to ensure a constant unwrapped phase on a constraining horizon. This idea is based on the fact that continuous seismic horizons are of time-stratigraphic significance. The horizon constraints can promise a correct unwrapped result on the constraining horizons and avoid the possible phase unwrapping errors propagating across a horizon. An unconformity represents a geologic time discontinuity, which is difficult to recover in an RGT volume by phase unwrapping. What’s worse, incorrect phase unwrapping on an unconformity will result in some discontinuities of unwrapped phase in the conformable data areas outside the unconformity. Interpreted unconformities are used as unconformity constraints to recover the discontinuities of the unwrapped phase at the constraining unconformities. As a test, our improved 3D graph-cut phase unwrapping method is successfully applied to the late Permian to early Triassic carbonate reservoirs in northern Sichuan Basin, southwest China. The results match well with the regional geologic background.