The invention discloses a ballastless track tunnel bottom upwarping control device and a construction method thereof. The control device comprises a plurality of vertical drill holes which are vertically drilled into a tunnel bottom surrounding rock from a roadbed slab after the construction of the roadbed slab is completed. The forming positions of the vertical drill holes are staggered with thelaying position of a ballastless track, and the inner walls of the vertical drill holes are provided with supporting pipes. The construction method comprises: vertically drilling the vertical drill holes into the tunnel bottom surrounding rock from the roadbed slab after the construction of the roadbed slab of the track is completed, and the forming positions of the vertical drill holes being staggered with the laying position of the ballastless track; laying the supporting pipes on the inner walls of the vertical drill holes, arranging strain gauges on the supporting pipes, and conducting regular detection; and when the stress of the strain gauges tends to be stable, grouting and sealing the vertical drill holes. According to the invention, by using the difference between rigidity of a tunnel structure supporting system and rigidity of the vertical drill holes, a deformation space is provided for the tunnel bottom surrounding rock through the inward deformation of the vertical drill holes, so as to achieve the goals of eliminating the upwarping of the tunnel bottom and controlling the deformation of the tunnel bottom.