Foodborne pathogens are predominant factors affecting human health. Due to the species diversity of foodborne pathogens and the complicity and time-consuming of traditional techniques, a rapid and accurate foodborne pathogen detecting technology is urgently needed. For the traditional infrared spectroscopic techniques, samples need to be lyophilized (about 2 days) before being pressed into a KBr pellet. Therefore, it is not conducive to fast and high-throughput detection. In this study, a developed ZnSe film transmission method was employed to drop samples on the ZnSe window directly, and an in-situ detection was carried out after low-temperature drying without long lyophilization process. The whole detection process was completed within 50 min. Meanwhile, only small sample volume (10 μL) was needed and the adverse effects of KBr pressed pellet method (e. g., size of abrasive particles, thickness error, easy fragmentation and moisture absorption) were avoided. In the meantime, by comparing the four foodborne pathogens (Escherichia coli DH5α, Salmonella enteritidis CMCC 50041, Vibrio cholerae SH04, Staphylococcus aureus SH10) with the conventional KBr pressed pellet method, the number of peaks in second derivative infrared (SD-IR) spectroscopy obtained by the ZnSe film transmission method (1 500~900 cm^-1) significantly increased (ZnSe film transmission method: 81, KBr pressed pellet method: 58) under the same peak threshold detection (transmittance >0.05%) and broad single peaks or inconspicuous double peaks in the KBr pressed pellet method could be split into two or more peaks (Escherichia coli DH5α: 1 441, 1 391, 1 219 cm^-1 etc; Salmonella enteritidis CMCC 50041: 1 490, 1 219, 1 025 cm^-1; Vibrio cholerae SH04: 1 441, 1 219 cm^-1; Staphylococcus aureus SH10: 1 491, 1 397, 1 219 cm^-1) with higher peak intensity (1 119, 1 085, 915 cm^-1 etc.). Therefore, it had been demonstrated that spectral resolution and the signal to noise ratio in the ZnSe film transmission method were significantly improved. The in-situ infrared spectroscopy based on ZnSe film transmission method has great potential for the rapid and high-throughput detection of common foodborne pathogens in food.