A large number of studies have shown that propolis has positive effects in the treatment of type 2 diabetes mellitus (T2DM). However, there are have only been a few reports that are based on an ultra-high performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry (UPLC-Q-TOF-MS) analysis of the fecal metabolomics of ethanol extract of propolis (EEP) in the treatment of T2DM. The present investigation was designed to screen potential biomarkers of T2DM by the metabonomic method and to explain the possible anti-diabetes mechanism of EEP according to the changes in the biomarkers. The results showed that EEP improved the body weight (BW) of T2DM mice, lowered blood sugar levels, and significantly restored blood biochemical indicators related to T2DM, such as fasting insulin (FINS), homeostasis model assessment of insulin resistance (HOMA-IR), aspartate transaminase (AST), and alanine aminotransferase (ALT). Liver pathology showed that EEP reversed liver damage caused by T2DM. Metabolomics data identified 27 potential biomarkers in fecal samples. EEP effectively regulated the dysfunction in the metabolic pathways of glycerophospholipids, sphingolipids, riboflavins, and sterol lipids caused by T2DM. In summary, our research results revealed positive effects of EEP in the treatment of T2DM and provided potential candidate markers for further research and in the clinical treatment of T2DM.