Virtual reality (VR)-based measurement systems have recently been developed to quickly measure individual head-related transfer functions (HRTFs) with arbitrary head movements. However, these systems are usually limited to estimate 2D HRTFs with a fixed distance between the loudspeaker and the subject. In the present study, a mixed reality (MR)-based mobile measurement system for fast estimation of distance-dependent HRTFs (3D HRTFs) is proposed. During the measurement, subjects can not only rotate their heads but also move their bodies towards or away from the loudspeaker. Additionally, the qualities of estimated HRTFs are calculated and displayed to subjects in real-time. Furthermore, the influences of the MR head mounted display (HMD) on the far- and near-field HRTFs are objectively evaluated.