The mouse Magnetocardiogram’s (MCG) accurate measurement is of the utmost importance for studying heart diseases. However, most of the currently used measuring instruments are Superconducting Quantum Interference Devices (SQUIDs), which are quite problematic. For example, they have a large scale, are expensive, and are difficult to widely promote. To address these issues, we present a mouse MCG measurement system using a Spin-Exchange-Relaxation-Free (SERF) atomic magnetometer. The measurement system mainly consists of a magnetic sensor, a mouse fixation device, a magnetically shielded device, and a data acquisition and processing module. We fabricated a single-axis SERF rubidium atomic magnetometer with a sensitivity of 20 fT/ √ Hz to serve as the system’s magnetic sensor. We also conducted experiments on the mouse MCG signals. Using power line harmonic modeling and wavelet threshold filter processing, we processed the raw signal and obtained an <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</i> -peak amplitude of 5 pT; moreover, the <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</i> -, <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">QRS</i> -, and <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</i> -waves were clearly visible. We also performed heart rate monitoring on mice at different ambient temperatures. Finally, we conducted a comparative analysis of related systems to illustrate the proposed system’s advantages for mouse MCG signals. This work demonstrates that the SERF atomic magnetometer is compatible with the long-term detection needs of the mouse cardiac magnetic field.