Objective Analyzing the transesophageal echocardiographic features of patent foramen ovale (PFO) in the cryptogenic stroke(CS) and the migraine(MA) to provide anatomical basis for etiological analysis. Methods From January 2018 to April 2021, the patients of CS and the patients of MA who had been diagnosed with PFO by the transesophageal echocardiography and the contrast transesophageal echocardiography at Beijing Tiantan Hospital affiliated to Capital Medical University were enrolled. All patients’ data were collected including age, gender, smoking, drinking, the width of inlet and outlet of PFO, swing of septum primum, length of PFO’ tunnel, thickness of septum secundum, and the degree of right-to-left shunting(RLS) from PFO at resting state and Valsalva maneuver. A propensity score matching analysis was performed at a ratio of 1: 1. Features of transesophageal echocardiographic were compared between the groups after matching. Logistic regression analysis were conducted to explore the factors of cryptogenic stroke. Results The two matched groups had no significant differences in age, gender, smoking, drinking (P>0.05). At the resting state and Valsalva maneuver, the inlet and outlet width of PFO measured by TEE in the CS were larger than those in the MA, the difference were statistically significant (P＜0.05). The thickness of the secondary septum, the length of PFO’ tunnel and the swing of primary septum between two groups were not significant different (P＞0.05); The PFO-RLS between two groups was not significant different (P＞0.05); Multivariate analysis showed that inlet and outlet of PFO at Valsalva maneuver were independent predictors of cryptogenic stroke. Conclusions The width of inlet and outlet of PFO in the cryptogenic stroke with PFO were larger than those in migraine with PFO, especially at Valsalva maneuver. The inlet and outlet of PFO at Valsalva maneuver examined by transesophageal echocardiography in patients of cryptogenic stroke were lager than those in migraineur.