We aimed to establish a method for the rapid identification of three common Gram-positive bacteria (Bacillus cereus, Listeria monocytogenes, and Micrococcus luteus) associated with foodborne diseases. MALDI-TOF-MS was used to determine the effects of sample pretreatment, culture medium, and culture time on the identification results. Then, MALDI-TOF-TOF-MS was used to establish an optimized method and further explore the effects of culture time on secondary proteins. Among the three sample pretreatment methods, formic acid extraction outperformed direct transfer and extended direct transfer, resulting in more protein peaks and higher peak intensity in B. cereus culture samples. However, with different culture times (1–7 d), ion peaks of all bacterial proteins were relatively stable according to MALDI-TOF-TOF-MS data. The protein peaks of B. cereus (1430 m/z), L. monocytogenes (2100 m/z), and M. luteus (2140 m/z) were split into small ion peaks at 1162, 1465, and 1625 m/z, respectively. After 7 d of culture, the secondary spectra, peak intensities, and peak values of formic acid-treated samples were relatively stable, indicating that secondary protein peaks were less affected by culture time. It provides a new approach for the routine identification and market supervision of food safety in China.