Among patients who receive heart transplantation (HTx) after long-term mechanical circulatory support (MCS), some show executive cognitive dysfunction without a history of stroke. Fifty HTx patients (19 patients on MCS for longer than 3 months before HTx and 31 patients without MCS as control group) were enrolled in the study. All subjects were men aged between 20 and 59 years without a history of stroke. Patients with MCS were divided into two groups: the AH-Thr group (n = 11), in which thrombus was detected in the left ventricular assist device (LVAD) and quickly removed (mean 3.3 times); and the AH group (n = 8), in which there was no detectable thrombus in the LVAD. The Trail Making Test (TMT) and the Wisconsin Card Sorting Test (WCST) were administered. The AH-Thr group showed poorer cognitive performance both in the TMT part B, with longer completion time (p < 0.05 versus the other two groups), and in the WCST, with more perseverative errors (p < 0.001 versus the other two groups). These data indicate that patients in the AH-Thr group showed executive cognitive dysfunction in set-shifting ability, suggesting frontal lobe damage. The conditions that facilitate thrombus formation in the LVAD may induce executive cognitive dysfunction without stroke.