The invention discloses a calibration system and a calibration method suitable for an on-missile inertial assembly of a small-sized guided missile. The calibration system comprises a joint robot, a clamp, a test platform, a remote control cabinet and the like, wherein the joint robot can clamp and fix a tested missile through the special clamp, and the remote control cabinet controls the joint robot to grab the tested missile to reach different positions and postures; at the same time, the joint robot is provided with an angle reference, and test and calibration of the on-missile inertial assembly are realized through comparison between the angle reference and output of the inertial assembly. The calibration system of the invention has the beneficial effects that: test and calibration of the on-missile inertial assembly can be completed under the whole missile condition, a stable, reliable, safe and convenient platform for test and calibration of the on-missile inertial assembly is provided, and the problem that a calibration process of the on-missile inertial assembly is complex at present is solved.