Margot has discovered and studied several binary asteroids with radar and optical telescopes. In 2000, he obtained the first images of binary near-Earth asteroids and described formation of the binary by a spin-up process. Margot and his research group have studied the influence of sunlight on the orbits and spins of asteroids, the Yarkovsky and YORP effects.
In 2007, Margot and collaborators determined that Mercury has a molten core from the analysis of small variations in the spin rate of the planet. These observations also enabled a measurement of the size of the core based on a concept proposed by Stan Peale.
In 2012, Margot and graduate student Julia Fang analyzed Kepler data to infer the architecture of planetary systems. They described planetary systems as "flatter than pancakes." They also showed that many planetary systems are dynamically packed.