The invention relates to a steel tube shelter pile stratum reinforcing system used when a tunnel traverses a structure and a construction method of the steel tube shelter pile stratum reinforcing system. Affected by the surroundings, the tunnel is likely to be limited by site conditions and surroundings when the tunnel traverses the structure, and for example, when the horizontal clear distance between the tunnel and the structure is insufficient or the tunnel downwards traverses the structure, no implementation conditions exist for conventional cast-in-situ bored pile type shelter piles. According to the steel tube shelter pile stratum reinforcing system used when the tunnel traverses the structure and the construction method of the steel tube shelter pile stratum reinforcing system, steel tube shelter piles are arranged between the existing structure (basement) and the undercrossing tunnel in rows, the bottoms of the steel tube shelter piles go deep into the positions below the arc bottom of the tunnel by a certain distance, the steel tube shelter piles are obliquely or perpendicularly beaten in, and the top portions of the steel tube shelter piles are connected into a whole through pile top crown beams; and between the steel tube shelter piles and the structure (basement), sleeve valve tubes are arranged in rows, the bottoms of the sleeve valve tubes go deep into the positions below the structure (basement) by a certain distance, and track grouting is carried out. The steel tube shelter pile stratum reinforcing system used when the tunnel traverses the structure and the construction method of the steel tube shelter pile stratum reinforcing system have the beneficial effects that the floor space is small, construction is flexible, and requirements of all kinds of environments can be met; and the structure reinforcing treatment requirement under various situations can be met.