Shoreline trajectory analysis improves the understanding of the correlation between clinoform architecture, shoreline and shelf-edge development, and sea-level changes. This study uses cores, well-logs and seismic data to investigate the depositional architecture and shoreline migration paths of early-mid Miocene deltaic clinoforms in the northern Pearl River Mouth basin, South China Sea. Five clinoform types are observed, including sigmoidal, oblique, tangential oblique, parallel oblique and sigmoidal-oblique clinoforms. Both the rollovers of deltaic clinoforms in seismic sections and the transitional points between delta plain and delta front deposits in well correlation cross-sections can be used as the indicators for shoreline positions, provided that there are no significantly extended subaqueous deltas. This allows for the identification of three shoreline trajectory types from a single clinoform set and three major stages from the net shoreline trajectory for multiple clinoform sets. A landward-directed net shoreline trajectory and ascending shoreline trajectories dominate in Stage 1 (23.8 to 17.5 Ma) with sigmoidal clinoforms transitioning into parallel oblique clinoforms, suggesting a rise in third and fourth-order relative sea level. Stage 2 (17.5 to 13.8 Ma) displays flat or descending trajectories and an overall seaward-directed net trajectory with a change from parallel to tangential oblique clinoform, indicating a relative sea-level fall. The reoccurrence of sea-level rise in Stage 3 (13.8 to 10.5 Ma) was inferred by a landward migration of parallel oblique clinoforms. This study shows that shoreline trajectory and net shoreline trajectory plotted from both seismic and well data is consistent with the regional sea-level curves estimated from foraminiferal fossil records and the shelf-edge development, which can be used to estimate the third and fourth-order relative sea-level changes in passive margins with wide, low-gradient shelves. Furthermore, clinoform architecture and migration may have been controlled by the variations of subsidence/uplift and sediment supply produced by tectonic events.