Cryptogenic stroke (CS) accounts for 25% of ischemic stroke. The etiology of undetermined stroke is unclear leading to untargeted secondary prevention, high recurrence rate, so the clinical burden of cryptogenic stroke is substantial. Cardiac magnetic resonance (CMR) imaging can identify more occult cardiac embolism that cannot be identified by standard cardiac assessment based on its excellent spatial resolution and contrast, three-dimensional imaging capacity and ability to depict soft tissues, to accelerate the initiation of optimal secondary prevention and improve the prognosis of patients. This review summarizes the application of CMR in the field of CS in recent years. Based on the latest evidence of diagnosis and management strategies, this paper proposes a cardiac diagnostic examination plan for CS patients, thereby improving the secondary prevention strategy of CS patients and improving their quality of life.