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In this study, we investigated the effects of Cu doping on the performance of CoFeSiB amorphous microwires as the core of a fluxgate magnetometer. The noise performance of fluxgate sensors primarily depends on the crystal structure of constituent materials. CoFeSiB amorphous microwires with varying Cu doping ratios were prepared using melt-extraction technology. The microstructure of microwire configurations was observed using transmission electron microscopy, and the growth of nanocrystalline was examined. Additionally, the magnetic performance of the microwire and the noise of the magnetic fluxgate sensors were tested to establish the relationship between Cu-doped CoFeSiB amorphous wires and sensor noise performance. The results indicated that Cu doping triggers a positive mixing enthalpy and the reduced difference in the atomic radius that enhances the degree of nanocrystalline formation within the system; differential scanning calorimetry analysis indicates that this is due to Cu doping reducing the glass formation capacity of the system. In addition, Cu doping affects the soft magnetic properties of amorphous microwires, with 1% low-doping samples exhibiting better soft magnetic properties. This phenomenon is likely the result of the interaction between nanocrystalline organization and magnetic domains. Furthermore, a Cu doping ratio of 1% yields the best noise performance, aligning with the trend observed in the material’s magnetic properties. Therefore, to reduce the noise of the CoFeSiB amorphous wire sensor, the primary goal should be to reduce microscopic defects in amorphous alloys and enhance soft magnetic properties. Cu doping is a superior preparation method which facilitates control over preparation conditions, ensuring the formation of stable amorphous wires with consistent performance.