Abstract: At present, application of quantitative analysis methods to study the paleo-environment in estuary area is rare in China, particularly in Minjiang Estuary. The purpose of this paper is to establish the diatom-salinity transfer function in Minjiang Estuary for the future study of paleoenvironment in this area. The CCA analysis on the surface sediment diatoms from Minjiang Estuary showed that the salinity had the best interpretation for the changes of diatoms. Thus, the estuary and its adjacent sea areas can be divided into four areas. The distribution of diatoms in area I was affected by the coastal waters outside the estuary. The distribution of diatoms in area II was impacted by the intrusion of tidal seawater. The distribution of diatoms in area III was affected by both tide and runoff and the distribution of diatoms in area IV was mainly impacted by runoff. Removed the abnormal station and with model comparison, the optimal transfer function was determined as the Component 5 model under the WA-PLS model. The transfer function relationship was S(fitting)= 0.25 + 1.007S(real), and the average error of 2.76 was used as the compensation to improve the transfer function accuracy.