The separation phenomenon of light and heavy ions was widely observed experimentally in the vacuum arc discharge with multi-component composite cathode. In this work, a two-dimensional axisymmetric multi-fluid model is used to study the separation mechanism in the multi-component composite cathode vacuum arc. The multi-component vacuum arcs are simulated as a whole which includes separate cathode spot jets, the mixing region, and common arc column. The results show that the plasma jets originated from the separate cathode spot mix together to form a common arc column after a certain distance from the cathode. Due to the rapid increase of ion temperature dozens of times in mixing region of cathode spot jet, the effect of pressure gradient becomes far greater than that of the collisions between light and heavy ions. This leads to a shift in the predominant ion motion mechanism from ion–ion collision (single cathode spot jet region) to pressure expansion (the mixing region). Finally, the light ions gain higher velocities under pressure expansion. In addition, the effect of thermal conductivity and viscosity leads to the wider high temperature regions for light ions, thus making a wider distribution of corresponding ion flux. The numerical results are qualitatively consistent with the experimental results. This paper provides an insight into ion separation mechanism in the multi-component vacuum arc.