The invention provides a space mission trans-scale verification apparatus with magnetic lift comprehensive compensation and free base, comprising a free base system, a lifting wire comprehensive electrochemical compensation system, a maglev system, an experimental spacecraft system, a coordinated control system, a communication system and a control center; orbital motion of a space target is converted into expected similar motion of a surface free base according to trans-scale equivalent theory and similarity theory, the expected similar motion is tracked further through the free base, and kinematic equivalency is achieved accordingly; a spatial micro-gravity motion environment is reproduced by a hybrid gravity compensation method combining lifting-wire-based lifting compensation and magnetic levitation, surface reproduction of a space mission is achieved, and surface complete process verification is completed for the space mission.