Flocculation has a great influence on the biogeochemical cycle by altering the particle size, density and settling velocity of suspended particulate matter (SPM) from coastal to shelf sea areas. However, the flocculation process in the shelf sea areas of China has not been systematically studied. In this study, the influencing mechanism of the North Yellow Sea cold water mass (NYSCWM) on the distribution and flocculation process of SPM is studied based on a comprehensive investigation during the summer of 2016. The results revealed that the mass concentration and turbidity of SPM showed a decreasing trend from coastal to offshore areas and an increasing trend from surface to near-benthic layers. Sediments from the Shandong subaqueous clinoform that were resuspended by the tidal mixing effect were the main source of inorganic SPM in the North Yellow Sea in summer. The existence of the bottom cold water mass enhanced the thermocline and pycnocline in the North Yellow Sea shelf area. The pycnocline obstructed the vertical diffusion of nutrients in the NYSCWM, resulting in a subsurface maximum chlorophyll a (chl a) layer, which further contributed to the maximum subsurface volume concentration of SPM. Flocculation was ubiquitous in the study area and was the main reason for the asynchronous variability in the mass concentration, turbidity and volume concentration of SPM. Three different kinds of flocculation mechanisms were identified, including the effects of biological activities in water masses above the NYSCWM, physicochemical effects in the near-benthic nepheloid layer within the NYSCWM, and their combined effects in shallow coastal areas. The flocculation of SPM enhanced the transport of particles from the surface to the bottom of the water column and made an important contribution to the formation of the North Yellow Sea mud deposit. •The CWM changed the marine physical and biological environments, resulting in variations in SPM flocculation conditions.•Three flocculation mechanisms, dominated by biological activity, physicochemical effects and their coeffects are proposed.•The flocculation processes of SPM play important roles in the formation of mud deposits in the North Yellow Sea.