A high-resolution seismic interpretation was executed to analyze the three-dimensional (3D) variation in canyon morphology, to deduce the main sedimentary processes and controls on submarine canyon evolution. Our study focuses on the 17 slope-confined canyons in the Shenhu Area within the Pearl River Mouth Basin. Quantitative analysis of geomorphologic parameters reveals significant spatial differences between the western (C1–C9) and eastern (C10–C17) canyons. The western canyons, located closer to the shelf-edge delta, exhibit greater sizes, higher reliefs, and dendritic or narrow, singular heads; the eastern canyons, situated farther from the delta, display shorter lengths, lower reliefs and arcuate, singular heads. Seismic stratigraphic analysis and seismic attribute mapping of the Quaternary succession indicate that the western canyons experienced higher rates of landward migration and more pronounced morphological changes over time, while the eastern canyons underwent subtler morphological changes, characterized by relatively stable and lower rates of canyon head migration. Based on the spatio-temporal variability of canyon morphology and shelf-edge architecture, we propose a four-stage evolutionary model for submarine canyons along the shelf-margin settings during the Quaternary: (1) active faulting led to widespread slope failure (2.58 Ma); (2) slow upslope migration of canyon heads by retrogressive erosion (2.58–1.2 Ma); (3) asymmetric sediment supply to the western and eastern canyons from the prograding delta in the northwest (1.2–0.4 Ma); (4) landward shift of deltaic shoreline and reworking by strong ocean currents partially buried some western canyons (0.4 Ma–present). This model highlights the impact of shelf-edge architecture on canyon morphology and contributes to a more comprehensive understanding of the interplay of tectonic, sedimentary, and oceanographic factors controlling canyon evolution along the same continental margin.