By using RS and GIS technology, the ecological risk index (ERI) was constructed based on the analysis of land use change and structural characteristics in urbanization watershed of Songhua River in Harbin section. Afterwards, the spatial distribution and change characteristics maps of ERI obtained by using block Kriging were analyzed to reveal the spatial and temporal evolution characteristics, change rules and formation mechanisms of ecological risk based on land use under the background of urbanization, and to minimize land use risk during urbanization process. The results showed that during the past 18 years, moderate ecological risk level was major, while proportion of high ecological risk was the lowest, and the area of higher and lower ecological risk region changed most greatly; high and higher ecological risk were focused on urban region and the transition zone from urban to suburban region, while low and lower ecological risk mainly distributed in forestland with higher vegetation coverage, water bodies, grassland, shrub land and so on. Meanwhile, the transition zone from high to low ecological risk was very obvious. In addition, ecological risk became slightly worse in some region due to the transformation from cropland to residential and urban land, while it became slightly better in other regions because of the transformation from cropland to forestland; the center of gravity in lower ecological risk region shifted most greatly, while the shift was the smallest in high ecological risk region, namely 12.31 and 0.57 km respectively.