The topical optimization problem of three-dimensional transfer to Phobos is considered. In the first version of the Phobos-Grunt project, the combined propulsion system comprising low thrust (LT) jet engines was supposed to be used. Maneuvers near Mars and the return stage were implemented with the use of a big thrust (BT) engine. Later this promising scheme with combining BT and LT jet engines was rejected [3]; however, the problem of designing and optimizing combined propulsion schemes of interplanetary missions remains. On the one hand, this problem is related to the real mission to Phobos, which the Russian Federation is going to implement in the next few years. On the other hand, development of the methods of the interplanetary trajectory optimization is a question of present interest. In other studies of such problems, planetocentric parts of trajectories are usually neglected, and there is no through optimization of the whole mission. In this paper, as an example of such a problem, the problem of designing the expedition to Phobos with these features taken into account is solved by Pontryagin’s extremal design method. Namely, the cosmodynamics problem is formalized as an optimal control problem; then the boundary problem of Pontryagin’s maximum principle is solved numerically by the shooting method. Certain trajectories are designed. Problems with the combined propulsion system and the efficiency of using LT in interplanetary expeditions are known for a long time. The possible gain due to using combined propulsion in comparison with using only BT engines is calculated for the mission to Phobos. We suppose that the spacecraft (SC) starts from the artificial Earth satellite orbit corresponding to a start from Baikonur between 2020 and 2030 and arrives at Phobos in some time. The total duration of an expedition is limited. The coordinates of the Earth, Mars and Phobos correspond to ephemeris DE424 and MAR097. The gravitational fields of the Sun, Earth and Mars are considered to be Newtonian. The moments of the SC start and finish are optimized. The SC is equipped with BT and LT engines. The control is realized by the value and the direction of a jet thrust vector. After the end of each trajectory part on which the propulsion system is used, it dumps instantly. The SC angular position on an initial starting circle and the moments of switching the thrust on and off are optimized. Weight losses are minimized. Rigid conditions of phasing are supposed at two trajectory end points. The SC lands on or flies up from the natural satellite. At the end of the mission, hit-the-point type condition of rendezvous with the Earth is considered. The SC and Phobos are supposed to be non-attracting material points; their coordinates and velocity vectors at the time of meeting coincide. The original problem has been solved, and specific numerical results are given. Pontryagin’s extremals are singled out as a result of solving a boundary value problem. The analysis depending on the problem parameters is carried out.