The flyby, set for Dec. 29, will be so close and fast the spacecraft will not be able to take any images, but it will gather accurate details of the moon's gravitational field to reveal new details of its internal structure, a release from ESA headquarters in Paris said Monday.
Small deviations in the spacecraft's velocity caused by the moon's gravity will be reflected in the spacecraft's radio signals to Earth, and scientists can then translate them into measurements of the mass and density structure inside the moon, the ESA said.
Earlier flybys have suggested the moon could be between a quarter and a third empty space, essentially a rubble pile with large spaces between the rocky blocks that make up the moon's interior.
Many scientists theorize Phobos and Deimos, the Red Planet's only moons, are either asteroids captured by Mars or were born from debris thrown up from giant impacts on Mars.
"By making close flybys of Phobos with Mars Express in this way, we can help to put constraints on the origin of these mysterious moons," said Olivier Witasse, ESA's Mars Express project scientist.