Very long baseline interferometry (VLBI) plays a crucial role in geodesy and astrometry, and it is also being successfully used in spacecraft tracking. Phase referencing VLBI is a technique that uses phase information rather than the traditional VLBI group time delay to achieve higher measurement accuracy. The newly developed source-frequency phase referencing (SFPR) VLBI has been proven to be a powerful method to eliminate errors, but for positioning purposes, only “core shifts” are left in SFPR. Therefore, in this paper, an in-beam SFPR (IB-SFPR) VLBI method based on SFPR is proposed to overcome the positioning deficiency in SFPR, and to achieve high positioning accuracy. The proposed IB-SFPR method is further researched in more detail and shown to have the ability to achieve high positioning accuracy. For the first Martian rover of China, the IB-SFPR is first applied in its positioning. The positioning results of the rover have shown that the 1σ formal position error is hundreds of meters, with a formal error of post-fitted phase time delay of about 1.3 ps. However, the position discrepancies among the results of IB-SFPR, the guidance, navigation and control system, and the visual localization are at kilometer level, which are mainly affected by the orbit error of the orbiter. Therefore, considering the external reference’s (the obiter) orbit error, the final positioning accuracy of the Martian rover is at the kilometer level.