Very late stent thrombosis is a life-threatening complication of implantation of drug-eluting stent (DES). The mechanisms are still unidentified. Stent malapposition is supposed to be one debated reason. Here we report a case of 33 months after DES implanted. Observed by optical coherence tomography, we detected a lipid-rich plaque with defective fibrous cap within the neointima and many local aneurysmal dilatations between stent struts, which mimic “malapposition” on the angiogram. These indicated that vulnerable plaque hidden in the neointima at the stent segment might be a potential mechanism of very late stent thrombosis after DES implantation.