In 2018, the Institute of Deep Sea Science and Engineering investigated the “HaiMa” cold seeps in the northwestern part of the South China Sea using R/V “TanSuoYiHao” with manned submersible “ShenHaiYongShi.” Ten dives were conducted to make seafloor observations at six cold seeps (HM‐1 to HM‐6). By combining multibeam echosounder data and seismic profiles, a systematic study was made to understand fluid migration, accumulation, and eruption and their impact on the ecosystem. Location of gas flares observed in the multibeam echosounder data obtained in 2016 and 2018 is different, indicating a year‐level spatiotemporal variation of the cold seep activities. Seafloor observation shows that massive carbonates occur in HM‐1 and HM‐5, indicating two long‐term existed cold seeps (several thousands of years). Mussels covered large areas of HM‐2, HM‐3, and HM‐6, suggesting young active seeps. Elevated seabed with broken edges, mud cones, clay pools, and sudden increased water turbidity and temperature was encountered in multiple areas, which are inferred to be associated with shallow gas accumulation and eruption. Methane content of the headspace gas from shallow sediment at HM‐2 is higher than 99.5% with δ13C‐CH4 of −71.5‰ to 72.3‰, indicating a biogenic gas origin. It is inferred that the gas is sourced by reservoirs at ~1,280 mbsf, which are characterized by low frequency in the seismic profiles. Gas migrates from the gas reservoir to the top of the Basel uplift along the slope. High‐angle faults are widely developed between 800 and 240 mbsf, facilitating gas migration from the top of the Basel uplift to the shallow sediment. Most of the faults did not reach the seafloor; therefore, gas accumulated at shallow depth exhibits bright spots in the seismic profiles. When the pore pressure overcomes the overburden sediment, fractures will be created for gas entering the water column. Gas emission provides a pressure release mechanism; therefore, most fractures did not reach the seafloor as observed in the seismic profiles. However, it is speculated that gas emission will stop with growth of gas hydrates and authigenic carbonates, which continuously decrease the permeability of the original fractures. Pressure will be built up, and new fractures will be generated, leading to the formation of new seeps. This mechanism is inferred to result in the spatiotemporal variation of cold seep activity and affects the development of the cold seep ecosystem.