Some of his notable works include:
- "Poland Under Socialist Rule: A History of the Country Since World War II" (1971)
- "From the Country of the Blest: The Soviet Union, 1917-1991" (1992)
- "The History of Poland" (co-authored with Zbigniew Herbert, 1980-1987)
- "The Origins of Modern Polish Politics: From the Partitions to World War II" (2004)
- "The Warsaw Uprising of 1944" (2009)
Modzelewski's work is known for its critical and often controversial analysis of Polish and Soviet history. He was one of the first scholars to challenge the official narratives of the Polish communist regime and its role in Polish society. His work has been translated into numerous languages and has influenced historians and scholars both in Poland and abroad.