Ion noise in output signal of klystrons was obtained by particle-in-cell method. The interactions between beam electron, ion, secondary electron and electromagnetic field are illustrated. The mechanism of ion noise is analyzed. It shows that phase fluctuation in output signal is caused by the change of the beam current DC velocity which is affected by the change of the amount of ions. The ion interacts with beam electron and has no equilibration state. The amount of secondary electrons is small and it has little effect on ion noise, but its behaviors reflect the process of ion noise. The amplitude fluctuation of output signal is caused by the change of beam velocity and beam radius. It is also affected by the ion behaviors.