The invention discloses a construction method of a total-prefabricated steel-concrete composite structure box girder. The method comprises the following steps: firstly prefabricating a roof, welding an upward extended shearing force connecting piece on a wave crest surface of a first corrugated steel sheet, filling a steel template or an airbag consistent with a wave trough shape in the wave trough as an inner membrane, and then binding a reinforcement cage of a reinforced concrete plate on the top of the first corrugated steel sheet, and finally depositing the concrete; secondly, prefabricating a bottom plate, placing the second corrugated steel sheet on a straight steel sheet in an alignment way, and connecting through a high-strength bolt; omitting the step of placing and connecting the second corrugated steel sheet when the bottom only adopts the straight steel sheet if the box girder size is small; and then prefabricating a corrugated steel web fixedly connected with the roof and the bottom plate; machining the end part of the web into a I-shaped structure connecting piece, or respectively welding outward extended connecting piece on the first corrugated steel sheet and a second corrugated steel sheet/straight steel sheet; and finally assembling in site. By use of the construction method disclosed by the invention, the inconsistent deformation problem between the steel structure and the concrete structure is effectively solved.