An apparatus for operating an airbag of an autonomous vehicle may include: an interior image sensor configured to capture an interior image of a vehicle; an input unit configured to receive collision prediction information from an autonomous driving system and the interior image from the interior image sensor; an airbag module installed at the front and side of the interior of the vehicle, and configured to deploy an airbag; and an airbag control unit configured to estimate the sitting position and dynamic behavior of the passenger from the interior image inputted from the input unit, estimate a collision status from the collision prediction information, determine an airbag to be deployed and a time to deploy the airbag according to the sitting position, and then output a deployment signal to the airbag module.