Mousnier was one of the few post-war French historians who was a detractor of both the Annales School and Marxist views of history. A right-wing Roman Catholic, Mousnier had a famous feud with the Soviet Marxist historianBoris Porchnev over whether peasant revolts in 17th-century France reflected class warfare or not. Mousnier denied there was much of idea of class in France during that period, which thus meant that there could have been no class war in 17th-century France as Porchnev maintained. In Mousnier's view, social classes did not emerge as an important factor in French society until the 18th century, with the coming of a more market-oriented economy. Mousnier also published the private papers of the chancelier Séguier in 1964. Mousnier's most notable claim to fame was his argument that early modern France was a "society of orders". In Mousnier's view, people in the period from the 15th century to the 18th century regarded honor, status and social prestige as far more important than wealth. As such, society was split vertically via social ranks rather than being split horizontally via class. Mousnier made it his life work to study how the relationships between different orders operated through networks of patronage. Mousnier referred to these relationships as maître-fidèle relations between those in the socially superior and those in the socially inferior orders. In general, Mousnier focused on elites in French society. In his view, differences between such orders as the land-owning noblesse d'épée and the bureaucratic noblesse de robe were more important than differences between the nobility and the peasantry. One of Mousnier's best known books, L'Assassinat d'Henri IV examined the climate of opinion and social context in 1610 France, in which a Catholic fanatic named François Ravaillac assassinated King Henry IV. Mousnier's conclusion was that there were numerous "potential Ravaillacs" in France who were looking for a chance to kill the King. Mousnier also produced the 1969 book Les Hiérarchies sociales that looked at how different civilizations such as Tibet, China, Germany, Russia and France were organized across time. Les Hiérarchies sociales was very critical of communist societies and those based on "technocratic orders".
Le XVIIIe siècle: l'époque des "Lumières" , 1953,.
Les XVIe et XVIIe siècles: la grande mutation intellectuelle de l'humanité: l'avènement de la science moderne et l'expansion de l'Europe, 1953.
Les XVIe et XVIIe siècles: les progrès de la civilisation européenne et le déclin de l'orient , 1954.
Progrès scientifique et technique au XVIIIe siècle, 1958.
L'assassinat d'Henri IV: 14 mai 1610, 1964.
Lettres et mémoires adressées au chancelier Séguier , 1964.
Problèmes de stratification sociales : deux cahiers de la noblesse pour les États géneraux de 1649-1651, 1965.
La participation des gouvernés à l'activité des gouvernants dans la France du XVIIe et du XVIIIe siècles, 1966. Social hierarchies: 1450 to the present
Fureurs paysannes: les paysans dans les révoltes du XVIIe siècle , 1967.
Les hiérarchies sociales de 1450 à nos jours, 1969.