The invention provides a method used for simultaneous detection of three food-borne pathogenic bacteria based on multicolor upconversion fluorescence labeling. According to the method, three upconversion materials with differentiable fluorescence spectrums are used for forming multicolor upconversion fluorescent nanoprobes via respective connection with aptamers of staphylococcus aureus, vibrio parahaemolyticus, and salmonella, and complementary oligonucleotide single chains of the aptamers are connected with magnetic nanoparticles so as to form nano-composites. When bacteria to be tested are in a detection system, double chain unwinding is realized because of specific binding of the pathogenic bacteria with corresponding aptamers; it is possible to realize simultaneous quantitative determination of staphylococcus aureus, vibrio parahaemolyticus, and salmonella by monitoring upconversion fluorescence signal strength at 477nm, 550nm, and 660nm, detection linear range ranges from 50 to 1000000cfu / ml, and detection limits are 25cfu / ml, 10cfu / ml, and 15cfu / ml respectively. The method is used for detection of pathogenic bacteria, is high in sensitivity, is rapid and convenient, and can be used for detection of the three pathogenic bacteria in food such as milk and shrimp meat; and results are accurate and reliable.