In general, great challenges make great presidents. There is no president who is widely seen as great who did not face a major challenge. Franklin Roosevelt faced two major challenges -- the Great Depression and WWII. His role in facing these challenges is why most historians see him as an all-time great.
Although FDR did not end the Great Depression, he is generally credited with helping the US get through that crisis. His leadership style is said to have helped make people more confident. That lessened the effects of the Depression. In addition, his New Deal is credited with setting up what historians see as a more just system in America with the government providing things like Social Security.
FDR's leadership helped bring the US through WWII as well. He was able to manage the relationships with the Soviet Union and with England in such a way as to maintain the alliance and win the war.
Because FDR was president during two of the most challenging periods in US history, he is seen as a great president.