Gastrointestinal tumors are one of the most common types of tumors. Emerging photoacoustic imaging technology can sharply capture the information of the nourishing blood vessels surrounding the tumors, which may give potential contributions to accurate clinical diagnosis. The matched vessel enhancement algorithm can effectively highlight the vessel network. However, the detection angle of in vivo photoacoustic endoscopic imaging is limited, which results in obvious vascular structure abnormalities. It is difficult for current enhancement algorithms to effectively enhance blood vessels. Therefore, a three-dimensional vascular enhancement algorithm was developed in this investigation that fuses the information on structure and intensity of the colorectal vessel of rats, based on a self-designed endoscopic photoacoustic imaging system. The results indicate that this algorithm can effectively improve the imaging effect, suppress edge burrs brought about by mechanical vibration, and obtain in vivo high-quality three-dimensional images of the colorectal vessel, indicating that it has potential value in basic medical research and clinical applications.