Seismic and logging while drilling (LWD) data, gas hydrate samples, and hydrate gas geochemical testing results acquired during the GMGS5 expedition in 2018 have been used to explore the geological occurrence and accumulation mechanism of gas hydrates in the eastern Qiongdongnan Basin (QDNB) of the northern South China Sea (SCS). A large gas chimney with diameter of 4 km associated with the Songnan Low Uplift and the Central Channel and characterized by acoustic blanking on the seismic profile was identified at site GMGS5-W9-2018 in the deep water QDNB. Seismic indications for hydrocarbon migration and gas hydrate accumulation including low frequency features, enhanced reflections, pull-ups/downs and the bottom simulating reflector (BSR) were recognized within the chimney area. Gas hydrates were confirmed to be deposited at the depth of 7–158 mbsf based on the coring and sampling results and pilot hole LWD anomalies, which showed a high resistivity, low density, high gamma rays, and elevated acoustic velocity. Leakage type gas hydrates with multiple geomorphology occurrence, including massive, layers, nodules, fracture filling and disseminated, were recovered at the top of the gas chimney, suggesting favorable conditions for the accumulation of gas hydrates in the eastern QDNB. Although methane was the dominant hydrocarbon gas in all hydrate-bound gases, heavier hydrocarbons (C2+) were also prevalent. C2–C5 hydrocarbons made up to ~21% of the hydrocarbon gases, indicating their thermogenic origin and close relationship with deep reservoirs. Due to the presence of the C2+ hydrocarbons, structure I and structure II gas hydrates may coexist at site GMGS5-W9-2018. The base of structure II gas hydrate stability zone (BSIIGHSZ) was ~42–44 m deeper than the base of structure I gas hydrate stability zone (BSIGHSZ). The hydrocarbon migration and hydrate accumulation were closely related to the gas chimney in conjunction with the Songnan Low Uplift and the Central Channel, which transported the deep thermogenic gas to the GHSZ, forming hydrates in the fractured clay-dominated fine-grained sediments. The fractures occurred in the strata were likely driven by pneumatic forces. Overpressure in the sediments derived from gas charging and accumulation through the gas chimney may have caused the fractures in the sediments that dissipated the hydrocarbons into the GHSZ. We propose a model of gas hydrate accumulation that may aid in the future exploration of gas hydrates in the QDNB of the SCS.