The effect of post-harvest treatment of Xiangfenyihao tomatos with endophytic strain 011 crude extract in comparison to sterile water on the fresh-keeping of tomatoes was investigated in this study. The results indicated that after 25-d storage, the decay rate of the tomatoes treated with crude extract significantly decreased by 52.17% compared to that with sterile water. The results also showed that crude extract treatment slowed the mass-loss rate, significantly delayed the decline in Vitamin c, reducing sugar, soluble protein and the titratable acid content, and satisfactorily maintained the flavor of tomato fruits during storage. The accumulation of malonic dialdehyde and increase of superoxide anion radical (?O2-) were significantly inhibited, integrity of the cell membrane was maintained, and activities of peroxidase (POD), catalase (CAT), superoxide dismutase (SOD), and phenylalanine ammonia-lyase (PAL) were significantly enhanced. Therefore, the crude extract satisfactorily maintained the nutritional and commercial value as well as significantly improved the preservation of tomatoes. These results provide a theoretical basis for biological control and fresh-keeping of fruits and vegetables after harvest.