Based on daily precipitation data from June to August during 1961-2013 from 77 weather stations, using the methods of precipitation concentration period, precipitation concentration degree and statistical regression, this paper studies the distribution and variation of the main flood season precipitation and the comparison between 2013 and 1998, and analyses influence of abnormal precipitation on crop yield. The results show that rain days in 2013 are more than other years in Heilongjiang. A wide range of continuous heavy rain is more intensive and earlier. The precipitation is abnormally more, getting to the extreme value in the past 53 years. There aren’t obvious spatial change characteristics in longitude or latitude. The areas with most precipitation are in Songnen Plain while the less rainfall areas are along the river basin. The temporal variation is in the style of less more less. The concentrated period of the severe rainfall is the first dekad of July, when the most precipitation is collected during the whole flood season. There are differences in temporal spatial distributions of precipitation in main flood season between 2013 and 1998.The amount and duration of precipitation in 2013 exceed the previous peaks in 1998, especially in Heilong River Valley. However the rainfall has some local features and sudden ones in 1998. By using FY 3A/MERSI satellite data and WOFOST crop model, this paper consistently monitors flooded crop planting area, and simulates crop yield in flooded regions, and on the basis of this, this paper evaluates the crop production losses. The sum of losses is 3.97×109 kg.