Abstract: As a national second-class protected animal, Gymnocypris przewalskii is a unique indigenous fish that plays an extremely important role in maintaining the biodiversity and ecosystem stability of Qinghai Lake. After long-term adaptation to plateau extreme environment, Gymnocypris przewalskii has formed the characteristics of tolerance to hypoxia, low temperature, high salt and poor nutrition, however, due to the global temperature rises, the temperature of Qinghai Lake has been gradually increasing year by year, which causing changes of the habitat of fish. In this study, scanning electron microscopy and hematoxylin-eosin staining (HE) were used to observe the intestinal microstructure of Gymnocypris przewalskii, and its dietary characteristics were analyzed by DNA metabarcoding. The results showed that the histological structure of the foregut, midgut and hindgut of Gymnocypris przewalskii was clear and the difference was obvious. From inside to the outside, it was composed of four layers: mucous membrane layer, submucosa layer, muscularis and serosa layer, however, due to the lack of muscularis mucosae, only three layers of membrane structure were visible under the light microscope. The researchers observed that intestinal cavity gradually decreased from foregut to the hindgut. The height of mucosal fold decreased significantly (P<0.05), and the width of mucosa fold increased significantly (P<0.05). The number of goblet cells, secretory pores and secretory granules also decreased. The results of 18S rDNA and rbcL gene DNA metabarcoding sequencing showed that 51656 OTU were obtained from the intestinal contents of Gymnocypris przewalskii. After removing the sequences of fish, bacteria, archaea and fungi, a total of 39031 OTU were identified, representing 43 phyla, 114 classes, 282 orders and 435 families. At the phylum level, the main phyla are Streptophyta (53.73%), Bacillariophyta (23.19%), p_ unclassified_ d_ Eukaryota (11.14%), Cercozoa (6.67%), p_ unclassified (1.93%) and Rotifera (0.67%). At the class level, the main classes were Bryopsida (35.79%), Bacillariophyceae (23.05%), Magnoliopsida (18.03%) and Chrysophyceae (3.36%). At the order level, the main orders were Cymbellales (22.60%), Hypnales (17.97%), Rosales (17.97%) and Pottiales (17.92%). At the family level, the main families are f_unclassified_o_Cymbellales (22.46%), Rosaceae (18.03%), Pottiaceae (17.99%), Amblystegiaceae (17.63%) and Chrysocapsaaceae (2.91%). It could be seen that the main food components of Gymnocypris przewalskii are Bryopsida, Bacillariophyceae, Magnoliopsida, Chrysophyceae, Cercozoa, Rotifera and unidentified species. In all food groups, Streptophyta, Bacillariophyta and Cercozoa species are the majority, accounting for a relatively large number. To sum up, the intestinal structure of Gymnocypris przewalskii has its own specificity and the common characteristics of omnivorous fish, and the DNA metabarcoding feeding analysis results also confirmed that Gymnocypris przewalskii belongs to omnivorous fish. Phytoplankton, zooplankton, benthic animals and many currently unknown species of food could be used as its food, feeding range is extremely wide, which is mutually adapted with its intestinal structure. This study provides a scientific basis for artificial breeding and further protection of Gymnocypris przewalskii by elucidating its intestinal structure and feeding characteristics.