Abstract: In order to study the characteristics of metabolites in Monascus cheese, Monascus cheese BC20 and Monascus cheese ZX-99 were used as experimental groups, and commercially available blue mold cheese and white mold cheese were used as control groups. The low molecular weight metabolites involved in the four cheeses were analyzed by non-targeted metabolomics. Metabolites that were only enriched in the experimental groups (VIP>1, P<0.05, FC>2) and had no significant difference between the experimental groups (VIP≤1, P≥0.05) were considered as the characteristics of Monascus cheese. The results showed that among the 2510 metabolites identified in positive and negative ion modes, 23 substances were preliminarily considered as characteristic metabolites of Monascus cheese. Eight of these substances, including cucurbitacin e, fusidic acid, quinapril, methyl dopa, orcinol, licoricesaponin h2, alfuzosin, and 25-desacetyl rifapentin had certain beneficial activities. Through comparison between the experimental groups and control groups, there were 10 identical differential metabolic pathways. The enrichment degree of the protein digestion and absorption pathway was relatively high, and the proportion of pathways related to amino acids was the largest. Among the differential metabolites involved in these two pathways, the substance contents of propionic acid, DL-tyrosine, homoharringtonine, 2-isopropylmalic acid, creatine, and succinic were significantly increased in the two Monascus cheeses (P<0.05). This study provides a theoretical basis for defining the Monascus cheese, regulating metabolic direction and enriching beneficial metabolites.