Filtration and cross-flow ultrafiltration (CFUF) was applied for the effective separation of NPs in the Yangtze Estuary. The physiochemical properties of NP were characterized, and their relationships with environmental factors were further studied in the present study. The results show that NP size in Yangtze Estuary ranged from 69.5 to 263.5 nm with the average value of 157.3 nm and Zeta-potential values ranged from -40.1 mV to 196.0 mV. NOC concentrations ranged from 0.3 mg/L to 1.5 mg/L and the average value was 0.7 mg/L. NOC account for 5.1% to 30.5% of DOC, with an average of 16.7%. The binding capacity of metals with NP in the Yangtze River Estuary was in the order of Zn > Cu > total Cr > Co > Ni > Mn > Fe > Li > Al > B > K > Ba > Sr > Mg > Ca > Na, which reveals that terrigenous input may be the main source of NOC in the Yangtze River. The binding capacity of NP with trace metal is generally higher than the conventional metallic element. There was no significant correlation between NP size and salinity, DOC, NOC, SPM and Zeta-potential, respectively. Compared to NOC and UOC, better correlation was investigated between DOC, salinity and NP bound trace metals.