In the present study, an endophytic fungus isolate FTJZZJ09, which isolated from the fresh bulbs of Fritillaria thunbergii Miq., was identified as Penicillium chrysogenum based on its morphological characters and internal transcribed spacer (ITS) sequence. After being cultured in the modified CzapeK-DoX medium (3 g/L maltose, 3 g/L peptone A, 0.1 g/L K2HPO4, 0.05 g/L KCl, 0.3 g/L NaNO3, 0.05 g/L MgSO4·7H2O, 0.001 g/L FeSO4·7H2O, pH 6.5), it can secrete antibacterial metabolites under the condition of 28°C in a rotary shaker at 160 r/min for 7 days. Three antibacterial compounds were isolated from the ethyl acetate extract of the fermentation broth by silica gel, they were elucidated as cyclo (Pro-Gly), cyclo (Pro-Val) and 2-acetyl-4 (3H) quinazolinone. All the three compounds could inhibit the growth of Bacillus subtilis with the minimal inhibitory concentration (MIC) value of 0.8, 0.8, and 0.4 g/L respectively, while they showed no apparent effects against the growth of Gram-negative bacteria.