This paper analyses measured Modaomen hydrological data and exhibits the temporal and spatial distribution of salinity and characteristics of fresh and salinity water mixing, as well as the correlation between salinity, water level and suspended sediment concentration in the Modaomen region. Based on the establishment of high-precision three-dimensional salinity mathematical model in Modaomen region, this paper calculates various engineering plans and examines the changes of flow field and tidal saltwater intrusion, which provides elementary base for implementation of the waterway regulation engineering. The study indicates that the salinity degree has a merely minor increase after projects indeed in the estuary to provide situation for tide intrusion. However, the influence is little and it fails to be the chief reasons for the depravation of tide intrusion in the Modaomen estuary recent years.