A system for determining a vehicle door axis adjustment amount may include a plurality of first setting jigs fixed to a sealing flange of a vehicle body and configured to adjust a position of a door with respect to the vehicle body in a vehicle width direction, a second setting jig configured to support the door and adjust a position of the door with respect to the vehicle body in an up and down direction, and an eccentricity measurement bolt configured to temporarily assemble a door hinge bracket of a door hinge mounted on the vehicle body with the door and measure eccentricity with respect to a hinge bracket bolt hole formed in the door using a gauge.