The knowledge of the interior structure (e.g., homogeneous, porous, or fractured) of Martian moons will lead to a better understanding of their formation as well as the early solar system. One approach to inferring the interior structure is via geodetic characteristics, such as gravity field and libration. Geodetic parameters can be derived from radiometric tracking measurements. A feasible mothership-CubeSat mission is proposed in this study with following purposes, (1) performing inter-sat Doppler measurements, (2) improving the understanding of Phobos as well as the dynamic model, (3) securing the mothership as well as the primary mission, and (4) supporting autonomous navigation, given the long distance between the Earth and Mars. This study analyzes budgets of volume, mass, power, deployment Δv, and link, and the Doppler measurement noise of the system, and gives a feasible design for the CubeSat. The accuracy of orbit determination and geodesy is revealed via the Monte-Carlo simulation of estimation considering all uncertainties. Under an ephemeris error of the Mars-Phobos system ranging from 0 to 2 km, the autonomous orbit determination delivers an accuracy ranging from 0.2 m to 21 m and 0.05 mm/s to 0.4 cm/s. The geodesy can return 2nd-degree gravity coefficients at an accuracy of 1‰, even in the presence of an ephemeris error of 2 km. The achieved covariance of gravity coefficients and libration amplitude indicates an excellent possibility to distinguish families of interior structures.