On the basis of statistical analysis of the characteristics of salt tide intrusion changes at different time scales in Modaomen Channel from 1998 to 2015, Spearman rank correlation analysis was used to identify the correlation between discharge, sea level, mean tidal range, maximum tidal level, minimum tidal level, rainfall and saltwater over-standard time. Principal component analysis was used to determine the contribution of each factor to salt tide intrusion activities. The results show that the salt tide intrusion of Modaomen Channel during the period from 1998 to 2015 shows the characteristic of two-stage change, taking the dry season of 2004—2005 as the demarcation point. In the first stage, salinity exceeding standard hours shows a “V” type change characteristic of first decreasing and then rising, while in the second stage shows a downward trend, which is conducive to the water supply safety in estuary area. The time of salinity exceeding standard seriously mainly concentrates from December to February of next year, and the change process is basically consistent with the interannual change process. Discharge, sea level and lowest tide level are significantly correlated with salinity exceeding standard hours, and pass 99% significance level test. While the correlation between sea level and salinity exceeding standard hours(negative correlation)is inconsistent with the theoretical results, which is affected by human activities. The main reason for the “V” type change of salinity exceeding standard hours in the first stage is the influence of natural factors(rainfall), while the overall decline of salinity exceeding standard hours in the second stage is due to the disturbance of human activities, such as water diversion for stemming salt tide, besides natural factors.