Seven shelf-incising submarine canyon systems are developed in the Makran accretionary prism, offshore Pakistan. This paper uses multibeam bathymetric data and multichannel seismic profiles to study the geomorphologic and infilling characteristics of E Canyon in the east of accretionary prism. The E Canyon extends nearly north–south from the upper slope to lower slope, the bottom of the canyon is located in 1000 to 3000 m water depth, the main axis extends about 55 km, and the width varies from 5 to 9 km. The E Canyon shows U-shaped concave features in the northern cross-section view and V-shaped concave features in the southern cross-section view. Two continuous erosion pools are developed at the fifth and third ridges of the southern segment, respectively. The steepest sidewall (with slopes of 25.75° and 40.47°) of E Canyon was found near the third ridge. The filling sequence of coarse channel lags, slump debris flows, stacked channel sands and mass transported deposits and turbidite deposits from bottom to top is developed in the northern segment of the canyon. Strong erosion is developed in the southern part of the canyon and there is no sedimentation inside. On the abyssal plain, the continuation of the E Canyon is clearly erosive. Our preliminary analysis shows that the factors controlling the evolution of E Canyon may include sediment gravity flow, tectonic activity, sea-level change, climate and onshore rivers activity. The correlation between evolution of E Canyon and gas hydrates was explored, and it is believed that the erosion of E Canyon plays a destructive role in hydrate accumulation. At the same time, the destruction of hydrate-bearing layer induces the escape and leakage of hydrocarbon-bearing fluid, leading to the development of pockmark on the sidewalls of E Canyon. And the evolution model of gas hydrate accumulation in the development area of E Canyon was established.