AbstractSuperconducting quantum interferometer device (SQUID) plays a key role in understanding electromagnetic properties and emergent phenomena in quantum materials. The technological appeal of SQUID is that its detection accuracy for the electromagnetic signal can precisely reach the quantum level of a single magnetic flux. However, conventional SQUID techniques normally can only be applied to a bulky sample and do not have the capability to probe the magnetic properties of micro‐scale samples with small magnetic signals. Herein, it is demonstrated that, based on a specially designed superconducting nano‐hole array, the contactless detection of magnetic properties and quantized vortices in micro‐sized superconducting nanoflakes is realized. An anomalous hysteresis loop and a suppression of Little–Parks oscillation are observed in the detected magnetoresistance signal, which originates from the disordered distribution of the pinned vortices in Bi2Sr2CaCu2O8+δ. Therefore, the density of pinning centers of the quantized vortices on such micro‐sized superconducting samples can be quantitatively evaluated, which is technically inaccessible for conventional SQUID detection. The superconducting micro‐magnetometer provides a new approach to exploring mesoscopic electromagnetic phenomena of quantum materials.