This paper extracted and verified the snow cover extent in Heilongjiang Basin from 2003 to 2012 based on MODIS Aqua and Terra data, and the seasonal and interannual variations of snow cover extent were analyzed. The result showed that the double-star composite data reduced the effects of clouds and the overall accuracy was more than 91%, which could meet the research requirements. There existed significant seasonal variation of snow cover extent. The snow cover area was almost zero in July and August while in January it expanded to the maximum, which accounted for more than 80% of the basin. According to the analysis on the interannual variability of snow cover, the maximum winter snow cover areas in 2003-2004 and 2009-2010 (>180 x 10(4) km2) were higher than that of 2011 (150 x 10(4) km2). Meanwhile, there were certain correlations between the interannual fluctuations of snow cover and the changes of average annual temperature and precipitation. The year with the low snow cover was corresponding to less annual rainfall and higher average temperature, and vice versa. The spring snow cover showed a decreasing trend from 2003 to 2012, which was closely linked with decreasing precipitation and increasing temperature.