Micro-optical coherence tomography (mu OCT) is a novel imaging approach enabling visualization of the microstructures of biological tissues at a cellular or sub-cellular level. However, it has been challenging to develop a miniaturized flexible endoscopic mu OCT probe allowing helical luminal scanning. In this study, we built a flexible endoscopic mu OCT probe with an outer diameter of 1.2 mm, which acquires three-dimensional images of the arterial microstructures via helical scanning with an axial and lateral resolutions of 1.83 mu m and 3.38 mu m in air, respectively. Furthermore, the depth of focus of the mu OCT imaging probe was extended two-fold using a binary phase spatial filter. We demonstrated that the present endoscopic mu OCT could image cellular level features of a rabbit artery with high-risk atheroma and a bioresorbable scaffold-implanted swine coronary artery. This highly-translatable endoscopic mu OCT will be a useful tool for investigating coronary artery disease and stent biology.