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The superconductor/magnetoresistance (SC/MR) mixed sensor has the advantage of ultra-high sensitivity, but it is only sensitive to unidirectional magnetic fields that are perpendicular to the superconducting flux-to-field transformation amplifier (SFTA). This inherent characteristic limits its applications in three-dimensional magnetic field detection. This paper presents a new architecture of the SC/MR mixed sensor with magnetic flux guides to realize three-dimensional magnetic field measurement. The finite element analysis method was used to confirm the performance of the mixed sensor, which theoretically proved the feasibility of three-dimensional magnetic field measurement and analyzed the influence of the magnetic field detection errors caused by the installation errors of MFGs. Finally, a mixed sensor composed of a whole-SFTA, four tunneling magnetoresistances, and two layers of MFGs was prepared, and experimental performances were obtained. Indeed, the mixed sensor can measure the three-dimensional magnetic field. This work is a meaningful contribution to the development of three-dimensional weak magnetic field detection.