Objectives The infection of digestive tract protozoa in tree shrews was investigated to evaluate its potential risks in public health and ensure the accuracy and reliability of tree shrews in biomedical researches. Methods 108 tree shrews were randomly selected from an experimental base of animal farming in Kunming on May 18 and July 20, 2024, and fresh fecal samples were collected from each of them. Direct smear method, saturated saline solution floating method, and Lugo's iodine staining method were used to detect fecal samples. The infection of digestive tract protozoa was analyzed. The environment of farming tree shrews was evaluated and the effects of the hygiene and density of farming on the rate of infection were studied. Results The tree shrews artificially domesticated under captive conditions were mainly infected with protozoa including flagellates, and the infection was very severe, with an average infection rate of 85% (92/108). Exposure to pollution sources and excessive density of farming led to a decrease in the immune system of tree shrews, making them more susceptible to infection with flagellates. Conclusions The environment of farming tree shrews is one of the important factors contributing to the infection with digestive tract protozoan. Improving the environment of farming tree shrews and enhancing the management of hygiene are necessary to reduce the risk of tree shrews being infected with flagellates.