His publications include:
- States, Nations, Sovereignty: Sri Lanka, India and the Tamil Eelam Movement (Sage, 1994)
- The Challenge in Kashmir: Democracy, Self-Determination and a Just Peace (Sage, 1997)
- Bosnia after Dayton: Nationalist Partition and International Intervention (Oxford University Press, 2002)
- Kashmir: The Roots of Conflict, Paths to Peace (Harvard University Press, 2003)
- Contested Lands: War and Peace in Israel-Palestine, Kashmir, Bosnia, Cyprus and Sri Lanka (Harvard University Press, 2007)
- Transforming India: Challenges to the World's Largest Democracy (Harvard University Press, 2013)
- Secular States, Religious Politics: India, Turkey, and the Future of Secularism (Cambridge University Press, 2018)
- Kashmir at the Crossroads: Inside a 21st-Century Conflict (Yale University Press, 2021)
Reviewing Kashmir: The Roots of Conflict, Paths to Peace, Sumit Ganguly noted an uneven, well-documented and an accurate dispassionate analysis of the origins of insurgency and the sentiments that gave birth to the Kashmir dispute. He noted Bose to display a "supple understanding of the political eddies and currents" that swirled in the pre-independence Kashmir. Notwithstanding the praises, he criticized the works as "far too chatty and anecdotal" in light of his noncritical reproduction of vast amounts of claims and assertions from partisan Kashmiri folks without cross-vetting them for reliability. Ganguly also criticized his willingness to believe that Pakistan will be conducive enough to partaking in his proposed solution to the conflict, which called for an all-stakeholders-dialogue between from both sides of the border, joint-acceptance of the Line-of-Control and a bilateral-management of the original unified state pending a political devolution in the Indian state of Jammu and Kashmir. He concluded that Bose's notion of a military dominated state that had fostered unyielding public hostility towards India (esp. on the Kashmir issue) of being a ''viable, honest, and sensible negotiating partner to be chimerical".[6] Another review praised the book for its highly objective and well-researched scholarship and deemed it to be a major contribution to Kashmir studies which may provide a valuable tool in settling the dispute.[7] Perry Anderson, in his essay The Indian Ideology, observes that while Bose's book is descriptive, its suggested solution is simply in favour of the status quo. He regards Bose as the leader of Indian scholars in diaspora who have not used their right of free speech any better than their counterparts in India.[8]
Robert G. Wirsing reviewed Kashmir: Roots of Conflict, Paths to Peace to be a remarkably "illuminating, interesting and valuable study'' that prescribed "one of the most substantial and compellingly articulated" consociational solution to the Kashmir dispute despite neglecting the strategic dimension of the dispute and going soft on the roles of religious identity in the prolongation of the conflict.[9]
A reviewer remarked that whilst Transforming India: Challenges to the World’s Largest Democracy was a "stimulating and distinctive addition to the wave of publications about the 'new India'" it paid too little attention to political economy and fell short of other masterpieces in the field of Indian contemporary history or political science.[10] Norio Kondo, reviewing the same book agreed with the broader sentiments but disagreed with Bose's observations as to the time span of the emergence of federalization. He held it to be the broad time span between 1967 and 1977 rather than to be 1989; a particular year as Bose had pinpointed. Kondo also felt that the book would have benefited from a greater emphasis on political economy and an analysis of the heterogeneous north-eastern-insurgencies which were missing. Notwithstanding these limitations; Kondo found the book to be valuable for understanding the gradual yet "long-term federalization of India into a decentralized union of autonomous states".[11]
