While at Harvard, Motl worked on the pp-wave limit of AdS/CFT correspondence,[clarification needed] twistor theory and its application to gauge theory with supersymmetry, black hole thermodynamics and the conjectured relevance of quasinormal modes for loop quantum gravity, deconstruction, and other topics.

In 2006, he proposed the weak gravity conjecture with Nima Arkani-Hamed, Alberto Nicolis and Cumrun Vafa.

[4] Motl writes a science and politics blog called "The Reference Frame: Supersymmetric world from a conservative viewpoint", in which he expresses his scientific and right-wing political opinions, including invectives as well as personal insults.

[7][8] He also describes himself as a "champion of the consistent histories interpretation of quantum mechanics",[9] and has strongly criticised Erik Verlinde's entropic gravity theory.

[10][11] In April 2022, Motl retired the blog, citing censorship pressures and general dissatisfaction.