There are at least two ways to answer this question.
In one sense, Germany and Japan lost the most in this war. They were each subjected to long occupations that completely transformed their countries. They had their old governmental systems destroyed and remade and had some changes made to their social systems as well.
In another sense, though, the Soviet Union was the country that was most clearly devastated by the war. Something like 13% of its population was killed in the war and many of its cities were destroyed. This was the highest death toll of any major power in the war.
One could argue that Germany suffered the most since it was destroyed as a political entity and also lost over 10% of its population in the war.