In order to achieve high-speed in vivo pathological diagnosis of the digestive tract， a design method for an endoscopic optical coherence tomography system with high-speed and stable imaging was proposed. Firstly， in order to realize high-speed endoscopic imaging， a high-speed endoscopic optical coherence tomography system was developed by using a 200 kHz swept source， and the hardware accelerated processing technology， combining field programmable gate array and graphics processing unit was used to realize real-time data processing. Secondly， in order to improve the stability of imaging， the pulse signal fed back by the encoder was used for system logic control， which effectively corrects the image drift. Finally， the stability and imaging speed of the system were tested and analyzed， and the colorectal imaging experiment was carried out in a mouse. The experimental results show that the real-time imaging speed of the system can reach 141 frame/s when the image size is 1 024×1 333 pixels， and under the logic control timing， the system image stability is improved from 87.0% to over 98.6%. The optical coherence tomography imaging results from the mouse colorectum are consistent with those of the pathological sections. The system developed in this paper is characterized by high-speed and stable imaging， which can clearly distinguish the tomographic structure of the mouse colorectal tissue in vivo and in real time. It is expected to provide a new diagnostic method for the real-time pathological diagnosis of body cavity diseases.