The invention relates to a construction method for penetrating through a tunnel of a backfilling soil section and a transition section. The construction method is characterized by comprising the following steps: step 1, draining water from a construction site, and lowering a water level to be 2.0m lower than a bottom elevation of the tunnel; step 2, digging the tunnel; constructing a right-line tunnel of the transition section in a small mileage direction and a large mileage direction; mechanically digging by adopting a bench cut method and constructing the tunnel according to a B-shaped fracture surface structure; after constructing to the backfilling soil section, constructing the tunnel at the backfilling soil section in the small mileage direction and the large mileage direction; mechanically digging by adopting a reserved core soil method; constructing the tunnel according to a C-shaped fracture surface structure; when the distance between working faces at two ends of a left-line tunnel or/and the right-line tunnel is 10m, pausing digging construction on the working faces of the left-line tunnel or/and the right-line tunnel in the large mileage direction; and continually constructing the left-line tunnel or/and the right-line tunnel in the small mileage direction in a unidirectional way until the tunnel is through. The construction method provided by the invention is simple in steps, convenient to construct and safe and reliable; and the construction quality can be guaranteed and requirements of urban rail traffic construction are met.