All the living organisms can synthesize various fatty acids, which exist in different carbon chain length, configurations and biological functions. These fatty acids are involved in many important physiological activities including anabolism, energy metabolism, and signal transduction. The living organisms are also capable of degrading and utilizing fatty acids via different oxidative pathways and β-oxidation is one of the most important oxidative pathways in both prokaryotic and eukaryotic cells. Research in the model organism Escherichia coli has provided the most complete view of fatty acids β-oxidation. In this review, the progress of fatty acids β-oxidation in E. coli and other bacterial species were summarized. By taking the phytopathogen Xanthomonas as an example, this review then introduced the oxidation pathway and regulation mechanism of the diffusible signaling factor (DSF)-family quorum sensing signal (mid-chain unsaturated fatty acids). Based on current results, the specific enzymes required for β-oxidation of very-long-chain fatty acids, 3-methyl-fatty acids, Δ2/Δ3-unsaturated fatty acids, and polyunsaturated fatty acids were proposed. Finally, the key scientific questions to be answered in this field were prospected. This review provides a solid foundation for further study of fatty acid β-oxidation pathway and the underlying mechanisms of bacterial pathogenicity.