With the widespread use of magneto-sensitive elements, magnetic shields are an important part of electronic equipment, ultra-sensitive atomic sensors, and in basic physics experiments. Particularly in Spin-exchange relaxation-free (SERF) co-magnetometers, the magnetic shield is an important component for maintaining the SERF state. However, the inherent noise of magnetic shield materials is an important factor limiting the measurement sensitivity and accuracy of SERF co-magnetometers. In this paper, both amorphous and nanocrystalline materials were designed and applied as the innermost magnetic shield of an SERF co-magnetometer. Magnetic noise characteristics of different amorphous and nanocrystalline materials used as the internal magnetic shielding layer of the magnetic shielding system were analyzed. In addition, the effects on magnetic noise due to adding aluminum to amorphous and nanocrystalline materials were studied. The experimental results show that compared with an amorphous material, a nanocrystalline material as the inner magnetic shield layer can effectively reduce the magnetic noise and improve the sensitivity and precision of the rotation measurement. Nanocrystalline material is very promising for inner shield composition in SERF co-magnetometers. Furthermore, its ultra-thin structure and low cost have significant application value in the miniaturization of SERF co-magnetometers.