The flyby on December 29 will be so close and fast that Mars Express will not be able to take any images, but instead it will yield the most accurate details yet of the Phobos's gravitational field and, in turn, provide new details of its internal structure, ESA said.
As the spacecraft passes close to Phobos, it will be pulled slightly off course by the moon's gravity, changing the spacecraft's velocity by no more than a few centimetres per second.
Earlier flybys, including the previous closest approach of 67 km in March 2010, have already suggested that 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.
Knowing the structure of the roughly 27 x 22 x 18 km Phobos will help to solve a big mystery concerning its origin and that of its more distant sibling, Deimos, which orbits Mars at approximately three times greater distance.
Also Read
"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.
In addition to probing the gravitational field of Phobos during its close approach, Mars Express will be making measurements of how the solar wind influences the moon's surface.
"At just 45 km from the surface, our spacecraft is passing almost within touching distance of Phobos," said Michel Denis, Mars Express Operations Manager.
Both the position of the spacecraft and the moon must be known to high precision in order to make the most accurate calculations of the moon's internal characteristics.
Furthermore, ground stations around the world will track the spacecraft for a total of 35 hours in the lead up to, during, and after the flyby to ensure that the position of Mars Express is precisely known.