His relationship with the East German state began to deteriorate, however, with his drama Die Umsiedlerin [de] (The Resettler Woman) which was censored in 1961 after only one performance.

The East German government remained wary of Müller in subsequent years, preventing the premiere of Der Bau (Construction Site) in 1965 and censoring his Mauser [de] in the early 1970s.

Among his better known works, other than those already mentioned, are Der Lohndrücker (The Scab), Wolokolamsker Chaussee (Volokolamsk Highway) Parts I–V, Verkommenes Ufer Medeamaterial Landschaft mit Argonauten (Despoiled Shore Medea Material Landscape with Argonauts), Philoktet (Philoctetes), Zement (Cement), Bildbeschreibung (Description of a Picture aka Explosion of a memory) and Quartett.

[11] In 2009, one of Europe’s leading intellectual publishing houses, Suhrkamp, issued the final three volumes in a twelve-volume edition of Müller's collected works.

[12] Müller adopted Brecht's notion of Kopien (German for "copying"), the practice of regarding texts by others as material to be used, imitated, and rewritten.

Thus, Müller's work in the theater marks the beginning of a tradition of densely poetic dramaturgy based in the logic of association, rather than linear "dramatic" narrative.

Jonathan Kalb, theater critic for The New York Times, describes Müller's legacy on theatre as replacing the "closed" didactical form of the Brechtian parable with "open" dramatic forms offering multiple meanings based, in Hans-Thies Lehmann's words, on a surreal "montage dramaturg ... in which the reality-level of characters and events vacillates hazily between life and dream and the stage becomes a hotbed of spirits and quotes outside any homogeneous notion of space and time.

"[13] In reference to Müller, Tony Kushner declared, "Write into the void, learn to embrace isolation, in which we may commence undistractedly our dreadful but all-important dialogue with the dead.

[19] In terms of plays turned into operas, Wolfgang Rihm created his version of Die Hamletmaschine in 1987,[20] Pascal Dusapin composed a Medeamaterial (fr) in 1992,[21] and Luca Francesconi's adaptation of Quartett (de) was premiered in 2011.

[22] The Slovenian industrial music group Laibach also collaborated with Müller in his lifetime, and released an album based on in his texts under the name Wir sind das Volk in 2022.