Bacterial secretion systems are sophisticated nanomachines that are used by bacteria for selective transport of macromolecules across membrane. These membrane protein complexes play critical roles in bacterial pathogenicity, antibiotic resistance and ecological adaptation. Hitherto, a total of nine secretion systems have been identified and named as type I to type IX secretion systems (T1SS-T9SS) according to the chronological order of discovery. Recent advances in X-ray crystallography, nuclear magnetic resonance and cryo-electron microscopy increased the understanding of the architecture and structure of these macromolecular machineries. That provided unprecedented views to explain the mechanisms of how secretion systems release the effectors to the extracellular environment or host cells. Herein, this review summarizes the best knowledge of the progress of bacterial secretion systems (T1SS-T9SS), with a focus on their structure and function. We also highlight major advances in novel antimicrobials targeting these large protein machineries. Finally, we provide new perspectives for the future studies about structure identification and drug screening of secretion systems.