- Quelling the people: the military suppression of the Beijing democracy movement, Oxford University Press, 1992.
- Praying for power: Buddhism and the formation of gentry society in late-Ming China, Harvard University Press, 1993.
- The confusions of pleasure: commerce and culture in Ming China, University of California Press, 1998.
- The Chinese state in Ming society, RoutledgeCurzo , 2005.
- Collaboration: Japanese agents and local elites in wartime China, Harvard University Press, 2005.
- Vermeer's hat: the seventeenth century and the dawn of the global world, Profile, 2008.
- The troubled empire: China in the Yuan and Ming dynasties, Belknap Press of Harvard University Press, 2010.
- Mr Selden's map of China: the spice trade, a lost chart and the South China Sea, Profile, 2013.
- Death by a thousand cuts, Timothy Brook, Jérôme Bourgon, Gregory Blue, Harvard University Press, 2008.
- The Asiatic mode of production in China, edited by Timothy Brook. M.E. Sharpe, 1989.
- Culture and economy: the shaping of capitalism in Eastern Asia, edited by Timothy Brook and Hy V. Luong, University of Michigan Press, 1997.
- Civil society in China, edited by Timothy Brook and B. Michael Frolic, M.E. Sharpe, 1997.
- China and capitalism: genealogies of sinological knowledge, edited by Timothy Brook and Gregory Blue, Cambridge University Press, 1999.
- Documents on the rape of Nanking, edited by Timothy Brook, University of Michigan Press, 1999.
- Nation work: Asian elites and national identities, edited by Timothy Brook and Andre Schmid, University of Michigan Press, 2000.
- Opium regimes: China, Britain, and Japan, 1839-1952, edited by Timothy Brook and Bob Tadashi Wakabayashi, University of California Press, 2000.