A highly sensitive superconductor/tunnel magnetoresistance (TMR) composite magnetic sensor was designed and fabricated to satisfy the demands of detecting weak magnetic fields down to the pT range at low frequencies. First, analysis of the 1/f noise provided an optimized design scheme for the TMR unit to reduce the noise level. Then, the key structural parameters of the superconducting flux transformation amplifier (SFTA) were optimized with focus on the bonding quality between SFTA and TMR units using the finite element method to enhance the magnetic field magnification factor. An SFTA–TMR composite method with secondary alignment and multi-step bonding was proposed to fabricate the composite magnetic sensor and ensure the designed bonding gap and alignment accuracy. Experiments showed that the magnetic field sensitivity reached 5 pT/Hz0.5 (@ 13 Hz), which is beyond the highest level of superconductor/TMR composite magnetic sensors reported to date and is a further step toward the application of weak magnetic field detection.