As a popular form of fruit consumption, fresh-cut watermelon is of great convenience for its consumers. Owing to the lack of comprehensive knowledge about the quality changes of fresh-cut watermelon during its shelf life, guidelines and standards are unavailable currently. To clarify the deterioration process and its underlying mechanism in fresh-cut watermelon, the sensory parameters, metabolomics, and microbial community of fresh-cut watermelon during a three-day storage at both room temperature (RT) and refrigerator temperature were systematically studied in this work. Results revealed that the whole property of the watermelon stored at refrigerator temperature kept stable, while pulps stored at RT had substantially deteriorated after 36 h. The decay was reflected in the significant decrease in soluble solid contents, firmness, pH, and color parameters in the sensory perspective. At the metabolic level, significantly declined malate, citrate, uridine, uridine 5-monophosphate, and amino acids, and increased ethanol and lactate contents, were observed as deterioration markers, which partially resulted from the activities of pyruvate dehydrogenase and alcohol dehydrogenase and the burst of genera Enterobacteriaceae and Leuconostocaceae. This study unveiled the underlying mechanisms of quality changes in fresh-cut watermelon under its primary storage conditions to provide fundamental information and potential clues for its quality control and preservation.