The invention discloses a prevention and control device for ballastless track tunnel bottom deformation and a construction method thereof. The prevention and control device is characterized in that after an inverted arch filling layer is constructed, before a roadbed slab is laid, a plurality of vertical drill holes are vertically punched at the tunnel bottom surrounding rock from the inverted arch filling layer, and supporting tubes are arranged on the inner walls of the vertical drill holes; the construction method comprises the steps that after the inverted arch filling layer is constructed, before the roadbed slab is laid, the vertical drill holes are vertically punched into the tunnel bottom surrounding rock from the inverted arch filling layer; the supporting tubes are laid on the inner walls of the vertical drill holes; strain gauges are arranged on the supporting tubes, periodic detection is performed; when the stress result of the strain gauges tends to be stable, grouting andsealing are performed on the vertical drill holes. The deformable and stress relief space is provided for the tunnel bottom surrounding rock in the tunnel construction stage, after the tunnel bottomdeformation tends to be stable, the roadbed slab is laid, the laid roadbed slab can prevent the tunnel bottom from arching up to the great extent, and the remediation and maintenance cost for later-period tunnel bottom arching can be greatly saved.