In July 2015, two sample strips (T1 and T2) were laid in the squid beach wetland of Min River Estuary, and five sampling sites were selected to collect sediment samples. Due to the harmful effects of heavy metals Co and V on human beings and animals, and few studies on Co and V in the intertidal zone of the Min River Estuary, the physical and chemical properties, spatial distribution characteristics of Co and V, and the degree of their pollution were studied to provide data reference for pollution research of Co and V. The results showed that the average concentrations of Co and V in the sediment were 15.19 mg/kg and 102.94 mg/kg respectively, which were higher than the background concentration in Fujian Province. Compared with other estuaries, the concentrations of Co and V were moderate. The contents of Co and V decreased slightly from the land to the sea. The ground accumulation index method showed that the Co content in the sediment was slightly polluted, and V showed no pollution. In addition, the potential ecological hazard coefficients of Co and V were 7.24-14.85 and 1.47-4.17 respectively, indicating that the potential ecological hazard was slight. Co and V in the intertidal sediments of the Min River estuary were mildly polluted.