Because of evolution for millions of years, microbial pathogens have developed specific strategies to manipulate host cell functions for their own benefits. Many of these measures involve interference with host immune responses, regulation of host cell cycle or induction of programmed cell death. During the past few decades, there has been remarkable progress in the understanding of microbial pathogens interfering with the host cell cycle and its putative role in diseases. Here, we review some pathogenic microorganisms arresting host cell cycle at different phages and their mechanisms, especially some pathogenic bacteria delivering effector protein into host cells to modulate the host function. Therefore, further research on the mechanisms of host cell cycle manipulated by pathogenic microorganisms can serve as a clue to understand host-pathogen interaction and its pathogenesis, which may be useful for the development of new drug targets and (or) vaccine candidates.