The start-stop behavior of air lubricated thrust micro-bearings was investigated. The dynamic air bearing force was calculated considering the air rarefaction effect. The asperity contact force between the rotor face and air bearing surface was calculated. The axial motion of the micro-bearing during the start-stop process was determined. The effects of surface roughness and angular acceleration were discussed. The results showed that an increase in the standard deviation of the asperity height generated an increase in the air film thickness and a decrease in the air bearing force, leading to an increase in both the asperity contact force and the contact time during the start-stop process.