We developed a micro-motor based miniature catheter with an outer diameter of 3mm for ultrahigh speed endoscopic optical coherence tomography (OCT) using vertical cavity surface-emitting laser (VCSEL) at a 1MHz axial scan rate. The micro-motor can rotate a micro-prism at 1,200-72,000rpm (corresponding to 20-1,200fps) with less than 5V driving voltage to provide fast and stable scanning, which is not sensitive to the bending of the catheter. The side-viewing probe can be pulled back for a long distance to acquire three-dimensional (3D) dataset covering a large area on the specimen. VCSEL provides high a-line rate to support dense sampling under high frame rate operation. With the use of a C++ based high speed data acquisition (DAQ) system, in vivo three-dimensional OCT imaging in rabbit GI tract with 1.6mm depth range, 11 mu m axial resolution, 8 mu m lateral resolution, and frame rate of 400fps is demonstrated.