The invention discloses a tunnel bottom backfill subgrade settlement prepressing method based on a large karst roof. The method includes that before primary supporting of a tunnel structure and secondary lining capping, a prepressing system is built through components like a steel pipe upright and a jack, the steel pipe upright is arranged on a backfill body surface layer subgrade concrete slab, the jack is mounted on the steel pipe upright and supports the karst roof, prepressing counterforce is acquired through loading by the jack, fine sand is filled in a steel pipe in order to improve stability of the steel pipe upright, in this way, prepressing reinforcement and settlement accelerating of a backfill subgrade in the karst are realized. A tunnel stable roof is utilized to apply counterforce for subgrade prepressing, counterforce action of the roof on the subgrade is realized by connecting the steel pipe upright with the jack, prepressing load is changed by adjusting the jack, and loading modes of nonuniform prepressing and phased prepressing are realized by building the prepressing system.