ABSTRACT Endoscopic Optical Coherence Tomography (OCT) can provide high‐resolution cross‐sectional images for internal organ tissues. Combining the endoscopic imaging with Optical Coherence Tomography Angiography (OCTA), information of blood vessels in superficial lumen tissues is expected to be acquired. However, in endoscopic OCT systems using proximal scanning probes, performance of OCTA encounters significant challenges due to non‐uniform rotational distortion (NURD) caused by the non‐constant rotation of the distal imaging unit. In this study, we proposed a registration method for endoscopic OCTA imaging in a proximally controlled OCT System. Global registration and A‐line registration were employed to correct the distortion caused by mechanical friction between the catheter sheath and torque coil. Experimental performances in both microfluidic channel and rat rectum show significant correction of NURD. Our study achieved the first implementation of endoscopic OCTA under a spiral B‐scan rotation scheme in a proximally controlled OCT system, facilitating clear visualization of blood flow.