The invention discloses a backfill protective structure and a protection method for a high voltage electric power pipeline at the top of a deep foundation pit. The backfill protective structure comprises a sand cushion, a cement aggregate chip layer and a reinforced concrete cover plate; the sand cushion is arranged below the high voltage electric power pipeline, and the cement aggregate chip layer is filled in a set range above the high voltage electric power pipeline; and the reinforced concrete cover plate is poured above the cement aggregate chip layer and in a range of covering the two sides of the high voltage electric power pipeline for a set distance. The protective structure disclosed by the invention has the beneficial effects that specific backfill protective measures are adopted according to structural styles of different structures and spatial position relationships between the tops of the structures and a pipeline, and the backfill protection problem on the high voltage electric power pipeline protected in situ and difficult to move and change during municipal engineering constructions such as urban rail transit construction and comprehensive development of underground space is appropriately solved.